Variant report

Variant	rs335428
Chromosome Location	chr5:176922643-176922644
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SRF	chr5:176922289-176923082	ECC-1	luminal epithelium:	n/a	chr5:176922688-176922706 chr5:176922687-176922705
2	JUND	chr5:176922446-176922747	A549	lung:	n/a	n/a
3	POLR2A	chr5:176919037-176923987	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr5:176921376-176922993	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr5:176922607-176922769	Hela-S3	cervix:	n/a	n/a
6	TEAD4	chr5:176922573-176922918	K562	blood:	n/a	n/a
7	POLR2A	chr5:176922506-176922682	A549	lung:	n/a	n/a
8	MXI1	chr5:176922566-176922740	HepG2	liver:	n/a	n/a
9	POLR2A	chr5:176921609-176925367	ProgFib	skin:	n/a	n/a
10	HEY1	chr5:176920762-176925766	K562	blood:	n/a	chr5:176924290-176924305 chr5:176924354-176924369
11	POLR2A	chr5:176920718-176925182	GM12878	blood:	n/a	n/a
12	CTCF	chr5:176922640-176922790	HPF	lung:	n/a	chr5:176922713-176922726
13	POLR2A	chr5:176922332-176922937	HepG2	liver:	n/a	n/a
14	JUN	chr5:176920923-176925966	K562	blood:	n/a	chr5:176921780-176921792 chr5:176921781-176921791 chr5:176923863-176923871 chr5:176923859-176923870 chr5:176921782-176921790 chr5:176923861-176923872 chr5:176921566-176921575 chr5:176924269-176924277 chr5:176924268-176924278 chr5:176923861-176923873
15	POLR2A	chr5:176922351-176922935	K562	blood:	n/a	n/a
16	NFIC	chr5:176921566-176922898	ECC-1	luminal epithelium:	n/a	n/a
17	CTCF	chr5:176922540-176922690	HRPEpiC	eye:	n/a	n/a
18	POLR2A	chr5:176920925-176925879	K562	blood:	n/a	n/a
19	SRF	chr5:176922403-176922937	H1-hESC	embryonic stem cell:	n/a	chr5:176922688-176922706 chr5:176922687-176922705
20	ATF2	chr5:176922386-176923413	H1-hESC	embryonic stem cell:	n/a	n/a
21	RUNX3	chr5:176922442-176922770	GM12878	blood:	n/a	n/a
22	SRF	chr5:176922551-176922791	HepG2	liver:	n/a	chr5:176922688-176922706 chr5:176922687-176922705
23	MAX	chr5:176922378-176925278	A549	lung:	n/a	n/a
24	CEBPB	chr5:176922587-176922829	H1-hESC	embryonic stem cell:	n/a	n/a
25	TEAD4	chr5:176922439-176922955	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr5:176919522-176925218	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAX	chr5:176922523-176922853	K562	blood:	n/a	n/a
28	POLR2A	chr5:176920625-176922930	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr5:176921134-176923039	HUVEC	blood vessel:	n/a	n/a
30	GTF2F1	chr5:176922521-176922848	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr5:176922600-176922750	AG09319	gingival:	n/a	chr5:176922713-176922726
32	POLR2A	chr5:176922326-176922860	Gliobla	brain:	n/a	n/a
33	TEAD4	chr5:176922430-176925969	K562	blood:	n/a	n/a
34	SMARCB1	chr5:176920859-176922786	Hela-S3	cervix:	n/a	chr5:176921781-176921790
35	POLR2A	chr5:176922369-176922804	Hela-S3	cervix:	n/a	n/a
36	TCF12	chr5:176922324-176923005	ECC-1	luminal epithelium:	n/a	n/a
37	CBX3	chr5:176922476-176923003	K562	blood:	n/a	n/a
38	CCNT2	chr5:176922617-176922739	K562	blood:	n/a	n/a
39	CHD1	chr5:176921126-176925242	IMR90	lung:	n/a	n/a
40	TEAD4	chr5:176922507-176922923	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr5:176922600-176922750	SK-N-SH_RA	brain:	n/a	chr5:176922713-176922726
42	POLR2A	chr5:176919141-176926267	K562	blood:	n/a	n/a
43	POLR2A	chr5:176921530-176925092	GM12892	blood:	n/a	n/a
44	MAZ	chr5:176919747-176925761	IMR90	lung:	n/a	chr5:176921985-176921995 chr5:176921861-176921871 chr5:176922286-176922295
45	EP300	chr5:176921474-176925207	ECC-1	luminal epithelium:	n/a	chr5:176923891-176923907 chr5:176922179-176922186
46	CTCF	chr5:176922580-176922730	AG04450	lung:	n/a	chr5:176922713-176922726
47	POLR2A	chr5:176922478-176922744	HCT-116	colon:	n/a	n/a
48	EBF1	chr5:176922267-176922675	GM12878	blood:	n/a	n/a
49	PML	chr5:176922200-176922681	K562	blood:	n/a	n/a
50	POLR2A	chr5:176922463-176922874	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:176920960..176922896-chr5:177025688..177028644,2	K562	blood:
2	chr5:176735682..176745085-chr5:176921866..176925758,11	K562	blood:
3	chr5:176827670..176832994-chr5:176921295..176926945,8	MCF-7	breast:
4	chr5:176922123..176922916-chr7:100033576..100034154,2	Hela-S3	cervix:
5	chr5:176922387..176924706-chr5:176979914..176982502,2	MCF-7	breast:
6	chr5:176431208..176433685-chr5:176921378..176924111,2	K562	blood:
7	chr5:176922579..176925417-chr5:176960443..176963610,5	K562	blood:
8	chr5:176733741..176736131-chr5:176921060..176924841,3	MCF-7	breast:
9	chr5:176920960..176923857-chr5:177025688..177028389,2	K562	blood:
10	chr5:176922040..176925610-chr5:177017064..177019499,4	K562	blood:
11	chr5:176736901..176740398-chr5:176920138..176924378,4	MCF-7	breast:
12	chr5:176737737..176740536-chr5:176922032..176926292,7	K562	blood:

Variant related genes	Relation type
PDLIM7	TF binding region
ENSG00000240211	Chromatin interaction
ENSG00000272459	Chromatin interaction
ENSG00000198055	Chromatin interaction
ENSG00000131187	Chromatin interaction
ENSG00000146067	Chromatin interaction
ENSG00000027847	Chromatin interaction
ENSG00000087206	Chromatin interaction
ENSG00000160813	Chromatin interaction
ENSG00000184840	Chromatin interaction
ENSG00000213347	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs234376	0.97[EUR][1000 genomes]
rs2544814	0.85[EUR][1000 genomes]
rs2630759	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs335429	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs335431	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs335462	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs337366	0.80[EUR][1000 genomes]
rs337368	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs337370	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs96656	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916108	chr5:176688459-177078723	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
2	nsv883158	chr5:176726635-176931706	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	120 gene(s)	inside rSNPs	diseases
3	nsv883160	chr5:176740996-176952919	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv1024444	chr5:176751921-177427715	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	142 gene(s)	inside rSNPs	diseases
5	nsv883161	chr5:176754722-176958397	Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
6	nsv1020334	chr5:176779108-176954933	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
7	nsv883164	chr5:176780545-177003616	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
8	esv1816147	chr5:176787037-176966509	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
9	nsv883166	chr5:176817636-176940384	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
10	nsv883170	chr5:176824137-176952919	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
11	nsv883173	chr5:176842474-176931706	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
12	nsv883174	chr5:176842474-176940384	Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
13	nsv883175	chr5:176842474-176952919	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
14	nsv883176	chr5:176843297-176924175	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
15	nsv1030965	chr5:176851182-176937654	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
16	nsv1026103	chr5:176851182-176942552	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
17	nsv1022832	chr5:176861503-176937654	Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
18	nsv1018088	chr5:176861503-176942552	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
19	nsv1028123	chr5:176861503-176949149	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
20	nsv537965	chr5:176861503-176949149	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
21	nsv883177	chr5:176868358-177003616	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
22	esv2752795	chr5:176898619-177488281	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
23	nsv883179	chr5:176912073-176926674	Genic enhancers Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
24	nsv883180	chr5:176912073-176937177	Genic enhancers Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs335428	PDLIM7	cis	Muscle Skeletal	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:176901600-176923000	Weak transcription	Brain Angular Gyrus	brain
2	chr5:176911000-176923000	Weak transcription	Dnd41	blood
3	chr5:176914800-176922800	Weak transcription	Fetal Kidney	kidney
4	chr5:176914800-176923600	Weak transcription	Pancreas	Pancrea
5	chr5:176916600-176923200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:176916800-176923800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
7	chr5:176917000-176922800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:176917800-176924200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr5:176918000-176923000	Weak transcription	Brain Hippocampus Middle	brain
10	chr5:176918400-176923000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:176918400-176923000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr5:176918400-176923000	Weak transcription	Brain Anterior Caudate	brain
13	chr5:176918400-176923600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:176918600-176923000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr5:176919400-176923000	Genic enhancers	K562	blood
16	chr5:176919600-176923800	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
17	chr5:176919800-176923000	Weak transcription	Fetal Brain Female	brain
18	chr5:176919800-176923200	Enhancers	Right Atrium	heart
19	chr5:176920000-176922800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr5:176920000-176923000	Enhancers	Left Ventricle	heart
21	chr5:176920000-176923000	Enhancers	Stomach Mucosa	stomach
22	chr5:176920000-176923400	Enhancers	Brain Germinal Matrix	brain
23	chr5:176920000-176924000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr5:176920200-176923000	Genic enhancers	Fetal Lung	lung
25	chr5:176920200-176923800	Enhancers	Fetal Brain Male	brain
26	chr5:176920400-176922800	Enhancers	Duodenum Mucosa	Duodenum
27	chr5:176920400-176923200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr5:176920400-176923600	Weak transcription	Thymus	Thymus
29	chr5:176920400-176924000	Enhancers	Primary B cells from peripheral blood	blood
30	chr5:176920400-176924000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr5:176920600-176922800	Genic enhancers	H1 Cell Line	embryonic stem cell
32	chr5:176920600-176923200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:176920600-176923400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:176920600-176923600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:176920600-176923800	Flanking Active TSS	Hela-S3	cervix
36	chr5:176920800-176924000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr5:176921000-176922800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:176921000-176922800	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr5:176921000-176923000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr5:176921000-176923000	Transcr. at gene 5' and 3'	A549	lung
41	chr5:176921000-176923400	Enhancers	Fetal Thymus	thymus
42	chr5:176921000-176923800	Enhancers	Primary T cells fromperipheralblood	blood
43	chr5:176921000-176923800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
44	chr5:176921200-176923200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:176921200-176923400	Transcr. at gene 5' and 3'	Osteobl	bone
46	chr5:176921200-176923600	Enhancers	Primary hematopoietic stem cells	blood
47	chr5:176921200-176923600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
48	chr5:176921200-176923800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr5:176921200-176923800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:176921200-176923800	Transcr. at gene 5' and 3'	Fetal Stomach	stomach

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