Variant report

Variant	rs2630759
Chromosome Location	chr5:176915669-176915670
allele	A/C/G/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	POLR2A	chr5:176914058-176916673	U87	brain:	n/a	n/a
2	POLR2A	chr5:176914120-176915723	K562	blood:	n/a	n/a
3	POLR2A	chr5:176915393-176915734	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr5:176914073-176915764	GM12892	blood:	n/a	n/a
5	POLR2A	chr5:176914052-176916677	U87	brain:	n/a	n/a
6	POLR2A	chr5:176914331-176915708	K562	blood:	n/a	n/a
7	POLR2A	chr5:176915647-176915679	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr5:176913905-176917463	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
PDLIM7	TF binding region

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

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

rs_ID	r²[population]
rs234376	0.92[EUR][1000 genomes]
rs2544814	0.81[EUR][1000 genomes]
rs335428	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs335429	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs335431	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs335462	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs337368	0.82[EUR][1000 genomes]
rs337370	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs96656	0.90[AMR][1000 genomes];1.00[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
rs2630759	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	chr5:176907000-176916000	Weak transcription	Thymus	Thymus
8	chr5:176907000-176921000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr5:176907200-176916200	Weak transcription	Stomach Mucosa	stomach
10	chr5:176907200-176920000	Weak transcription	Primary B cells from cord blood	blood
11	chr5:176907200-176921000	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr5:176907200-176921000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:176907200-176921200	Weak transcription	Small Intestine	intestine
14	chr5:176907200-176921800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr5:176907400-176916600	Weak transcription	Fetal Heart	heart
16	chr5:176908200-176917000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:176908200-176917600	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr5:176908200-176917600	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr5:176908200-176919400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:176908600-176916400	Strong transcription	Placenta	Placenta
21	chr5:176908600-176916600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr5:176908600-176916800	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr5:176908600-176917400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:176908600-176917600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr5:176908600-176918200	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr5:176908600-176918200	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr5:176908600-176919800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:176908600-176920800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:176908600-176921000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:176908600-176921000	Strong transcription	Fetal Intestine Small	intestine
31	chr5:176908800-176916600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr5:176908800-176917600	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr5:176908800-176918200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr5:176908800-176920200	Strong transcription	Fetal Lung	lung
35	chr5:176908800-176920200	Strong transcription	NHEK	skin
36	chr5:176909000-176917400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr5:176909200-176919600	Strong transcription	Osteobl	bone
38	chr5:176909400-176918200	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr5:176909600-176917200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:176909600-176919600	Strong transcription	Right Ventricle	heart
41	chr5:176910000-176917800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr5:176910000-176920800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:176910200-176916000	Strong transcription	Fetal Intestine Large	intestine
44	chr5:176910200-176916400	Strong transcription	Gastric	stomach
45	chr5:176910200-176917800	Strong transcription	HMEC	breast
46	chr5:176910200-176918200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
47	chr5:176910200-176918200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr5:176910200-176918800	Strong transcription	Aorta	Aorta
49	chr5:176910200-176919600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr5:176910200-176919600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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