Variant report

Variant	rs335462
Chromosome Location	chr5:176916516-176916517
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:69)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:69 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr5:176916400-176916550	HFF-Myc	foreskin:	n/a	n/a
2	POLR2A	chr5:176915833-176916640	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr5:176916460-176916610	BE2_C	brain:	n/a	n/a
4	CTCF	chr5:176916361-176916552	GM12878	blood:	n/a	n/a
5	POLR2A	chr5:176914058-176916673	U87	brain:	n/a	n/a
6	CTCF	chr5:176916321-176916593	MCF-7	breast:	n/a	n/a
7	CTCF	chr5:176916420-176916570	HCT-116	colon:	n/a	n/a
8	POLR2A	chr5:176915797-176917038	GM12878	blood:	n/a	n/a
9	CTCF	chr5:176916420-176916570	HRE	kidney:	n/a	n/a
10	POLR2A	chr5:176916109-176916660	HL-60	blood:	n/a	n/a
11	POLR2A	chr5:176916258-176916597	GM12891	blood:	n/a	n/a
12	CTCF	chr5:176916380-176916530	GM12878	blood:	n/a	n/a
13	POLR2A	chr5:176915850-176916712	GM12892	blood:	n/a	n/a
14	POLR2A	chr5:176915915-176916817	HUVEC	blood vessel:	n/a	n/a
15	CTCF	chr5:176916375-176916517	MCF-7	breast:	n/a	n/a
16	CTCF	chr5:176916359-176916545	GM19239	blood:	n/a	n/a
17	POLR2A	chr5:176915818-176917515	GM12892	blood:	n/a	n/a
18	CTCF	chr5:176916313-176916604	MCF-7	breast:	n/a	n/a
19	CTCF	chr5:176916400-176916550	HBMEC	blood vessel:	n/a	n/a
20	CTCF	chr5:176916380-176916530	AG09319	gingival:	n/a	n/a
21	CTCF	chr5:176916420-176916570	BE2_C	brain:	n/a	n/a
22	POLR2A	chr5:176916229-176916621	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr5:176916380-176916530	HBMEC	blood vessel:	n/a	n/a
24	CTCF	chr5:176916380-176916530	Hela-S3	cervix:	n/a	n/a
25	CTCF	chr5:176916353-176916557	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr5:176916380-176916530	GM12864	blood:	n/a	n/a
27	POLR2A	chr5:176916332-176916632	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr5:176916268-176916583	Hela-S3	cervix:	n/a	n/a
29	CTCF	chr5:176916380-176916530	WERI-Rb-1	eye:	n/a	n/a
30	POLR2A	chr5:176914052-176916677	U87	brain:	n/a	n/a
31	MYC	chr5:176916307-176916564	MCF-7	breast:	n/a	n/a
32	POLR2A	chr5:176915957-176916864	GM12892	blood:	n/a	n/a
33	RAD21	chr5:176916345-176916563	HepG2	liver:	n/a	n/a
34	POLR2A	chr5:176915908-176917065	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr5:176916308-176916532	A549	lung:	n/a	n/a
36	CTCF	chr5:176916400-176916550	NHDF-neo	bronchial:	n/a	n/a
37	POLR2A	chr5:176915820-176917061	K562	blood:	n/a	n/a
38	CTCF	chr5:176916380-176916530	HCPEpiC	choroid plexus:	n/a	n/a
39	CTCF	chr5:176916380-176916530	GM06990	blood:	n/a	n/a
40	CTCF	chr5:176916420-176916570	Hela-S3	cervix:	n/a	n/a
41	CTCF	chr5:176916400-176916550	HA-sp	spinal cord:	n/a	n/a
42	CTCF	chr5:176916480-176916630	GM12878	blood:	n/a	n/a
43	POLR2A	chr5:176916269-176916567	MCF-7	breast:	n/a	n/a
44	POLR2A	chr5:176915904-176916673	ECC-1	luminal epithelium:	n/a	n/a
45	CTCF	chr5:176916380-176916530	HepG2	liver:	n/a	n/a
46	POLR2A	chr5:176916507-176916686	Hela-S3	cervix:	n/a	n/a
47	CTCF	chr5:176916356-176916556	IMR90	lung:	n/a	n/a
48	POLR2A	chr5:176916158-176916719	HUVEC	blood vessel:	n/a	n/a
49	CTCF	chr5:176916460-176916610	HFF-Myc	foreskin:	n/a	n/a
50	CTCF	chr5:176916420-176916570	GM12870	blood:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:176831179..176832031-chr5:176916030..176916892,2	MCF-7	breast:

No data

Variant related genes	Relation type
PDLIM7	TF binding region
ENSG00000198055	Chromatin interaction
ENSG00000131187	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs234376	0.93[EUR][1000 genomes]
rs2544814	0.85[CEU][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2630759	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs335428	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs335429	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs335431	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs337368	0.83[EUR][1000 genomes]
rs337370	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs96656	0.93[AMR][1000 genomes];0.97[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
rs335462	PDLIM7	cis	Muscle Skeletal	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:176900600-176919200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:176901600-176923000	Weak transcription	Brain Angular Gyrus	brain
3	chr5:176902400-176920200	Weak transcription	Fetal Brain Male	brain
4	chr5:176905800-176916600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:176906400-176917200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr5:176906400-176918000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:176907000-176921000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr5:176907200-176920000	Weak transcription	Primary B cells from cord blood	blood
9	chr5:176907200-176921000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr5:176907200-176921000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr5:176907200-176921200	Weak transcription	Small Intestine	intestine
12	chr5:176907200-176921800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr5:176907400-176916600	Weak transcription	Fetal Heart	heart
14	chr5:176908200-176917000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:176908200-176917600	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr5:176908200-176917600	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr5:176908200-176919400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:176908600-176916600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:176908600-176916800	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr5:176908600-176917400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:176908600-176917600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr5:176908600-176918200	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:176908600-176918200	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr5:176908600-176919800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:176908600-176920800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:176908600-176921000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:176908600-176921000	Strong transcription	Fetal Intestine Small	intestine
28	chr5:176908800-176916600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr5:176908800-176917600	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr5:176908800-176918200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr5:176908800-176920200	Strong transcription	Fetal Lung	lung
32	chr5:176908800-176920200	Strong transcription	NHEK	skin
33	chr5:176909000-176917400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr5:176909200-176919600	Strong transcription	Osteobl	bone
35	chr5:176909400-176918200	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr5:176909600-176917200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr5:176909600-176919600	Strong transcription	Right Ventricle	heart
38	chr5:176910000-176917800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:176910000-176920800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:176910200-176917800	Strong transcription	HMEC	breast
41	chr5:176910200-176918200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr5:176910200-176918200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr5:176910200-176918800	Strong transcription	Aorta	Aorta
44	chr5:176910200-176919600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:176910200-176919600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr5:176910200-176919800	Strong transcription	Left Ventricle	heart
47	chr5:176910200-176920000	Strong transcription	NHDF-Ad	bronchial
48	chr5:176910200-176921200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr5:176910400-176918400	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr5:176910400-176920600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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