Variant report

Variant	rs17630607
Chromosome Location	chr3:158389860-158389861
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	CTCF	chr3:158389780-158389930	GM12871	blood:	n/a	n/a
2	POLR2A	chr3:158389464-158390742	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr3:158389532-158390889	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:158389479-158390945	GM12891	blood:	n/a	n/a
5	POLR2A	chr3:158389545-158390856	A549	lung:	n/a	n/a
6	POLR2A	chr3:158388424-158390772	PANC-1	pancreas:	n/a	n/a
7	GABPA	chr3:158389744-158390886	MCF-7	breast:	n/a	n/a
8	POLR2A	chr3:158389578-158390852	MCF-7	breast:	n/a	n/a
9	CTCF	chr3:158389860-158390010	HRE	kidney:	n/a	n/a
10	SIN3AK20	chr3:158389652-158391089	MCF-7	breast:	n/a	n/a
11	KAP1	chr3:158389580-158390932	HEK293	kidney:	n/a	n/a
12	TBP	chr3:158389853-158390797	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAZ	chr3:158389398-158390863	IMR90	lung:	n/a	chr3:158389586-158389597
14	POLR2A	chr3:158389496-158390782	GM18505	blood:	n/a	n/a
15	WRNIP1	chr3:158389652-158390329	GM12878	blood:	n/a	n/a
16	CTCF	chr3:158389760-158389910	GM06990	blood:	n/a	n/a
17	RCOR1	chr3:158389688-158390735	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:158389396-158390808	PANC-1	pancreas:	n/a	n/a
19	MTA3	chr3:158389803-158390799	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:158389814-158390878	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr3:158389641-158389907	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr3:158381091-158391011	PBDE	blood:	n/a	n/a
23	CTCF	chr3:158389780-158389930	A549	lung:	n/a	n/a
24	NR2F2	chr3:158389780-158390846	MCF-7	breast:	n/a	n/a
25	CTCF	chr3:158389528-158391125	A549	lung:	n/a	chr3:158390572-158390580 chr3:158390569-158390587 chr3:158390571-158390592
26	MXI1	chr3:158389379-158391135	IMR90	lung:	n/a	n/a
27	CTCF	chr3:158389860-158390010	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:158388083..158390320-chr3:158417482..158420125,2	MCF-7	breast:
2	chr3:158378888..158380588-chr3:158388656..158390307,2	MCF-7	breast:
3	chr3:158362274..158363819-chr3:158388698..158391198,2	MCF-7	breast:

Variant related genes	Relation type
LXN	TF binding region
ENSG00000168827	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1595027	1.00[CHB][hapmap]
rs16829044	1.00[CHB][hapmap]
rs16829064	1.00[CHB][hapmap]
rs16829102	1.00[CHB][hapmap]
rs16829105	1.00[CHB][hapmap]
rs1714522	1.00[CHB][hapmap]
rs17630980	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17642769	0.82[AMR][1000 genomes]
rs17643171	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs17697458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17698494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17699103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17699324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17699478	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs17699526	0.84[AMR][1000 genomes]
rs17700122	0.90[CEU][hapmap]
rs1978780	0.89[CHB][hapmap]
rs2196357	0.88[CHB][hapmap]
rs2279561	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs2279562	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs2304408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2307064	0.90[CEU][hapmap];0.84[AMR][1000 genomes]
rs28372852	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35057010	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3867391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55666734	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56075263	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56089835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56148431	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56167308	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56242377	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60942689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62286647	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62286649	0.80[ASN][1000 genomes]
rs62286650	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62286654	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62287938	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62288301	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62288303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62288305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62288306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62288307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62288344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62288345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441208	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs6441221	0.90[CEU][hapmap]
rs6776901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6777231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6804230	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7610009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7633713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv869644	chr3:158308783-158426343	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv3399089	chr3:158356055-158410094	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs17630607	GFM1	cis	Nerve Tibial	GTEx
rs17630607	GFM1	cis	Thyroid	GTEx
rs17630607	GFM1	cis	Esophagus Mucosa	GTEx
rs17630607	GFM1	cis	Artery Tibial	GTEx
rs17630607	GFM1	cis	Muscle Skeletal	GTEx
rs17630607	LXN	Cis_1M	lymphoblastoid	RTeQTL
rs17630607	LXN	cis	multi-tissue	Pritchard
rs17630607	GFM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158362800-158390000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:158364800-158391000	Strong transcription	Dnd41	blood
3	chr3:158376600-158390200	Strong transcription	HSMM	muscle
4	chr3:158385600-158390000	Weak transcription	Aorta	Aorta
5	chr3:158386200-158407800	Weak transcription	HepG2	liver
6	chr3:158386600-158390000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:158388600-158390600	Active TSS	Fetal Lung	lung
8	chr3:158388800-158390200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:158388800-158390600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:158388800-158390800	Active TSS	Fetal Intestine Large	intestine
11	chr3:158389000-158390000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:158389000-158390200	Strong transcription	HSMMtube	muscle
13	chr3:158389000-158390600	Active TSS	NHLF	lung
14	chr3:158389000-158390600	Active TSS	Osteobl	bone
15	chr3:158389000-158390800	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr3:158389200-158390000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr3:158389200-158390000	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr3:158389200-158390000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:158389200-158390000	Enhancers	Placenta Amnion	Placenta Amnion
20	chr3:158389200-158390200	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr3:158389200-158390200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr3:158389200-158390600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:158389200-158390600	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr3:158389200-158390600	Active TSS	A549	lung
25	chr3:158389200-158391200	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr3:158389400-158390000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr3:158389400-158390000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr3:158389400-158390000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:158389400-158390000	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr3:158389400-158390200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr3:158389400-158390200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:158389400-158390200	Flanking Active TSS	Duodenum Mucosa	Duodenum
33	chr3:158389400-158390200	Flanking Active TSS	HMEC	breast
34	chr3:158389400-158390400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:158389400-158390600	Active TSS	H1 Cell Line	embryonic stem cell
36	chr3:158389400-158390600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:158389400-158390600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:158389400-158390600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:158389400-158390600	Active TSS	Fetal Kidney	kidney
40	chr3:158389400-158390600	Active TSS	NH-A	brain
41	chr3:158389400-158390800	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr3:158389400-158390800	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr3:158389400-158390800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:158389400-158390800	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr3:158389400-158390800	Active TSS	Colonic Mucosa	Colon
46	chr3:158389400-158390800	Active TSS	Fetal Intestine Small	intestine
47	chr3:158389400-158390800	Active TSS	Rectal Smooth Muscle	rectum
48	chr3:158389400-158390800	Active TSS	Right Atrium	heart
49	chr3:158389400-158390800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr3:158389400-158391000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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