Variant report

Variant	rs7613489
Chromosome Location	chr3:46731303-46731304
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46730164..46732483-chr3:46734488..46736983,2	MCF-7	breast:
2	chr3:46711657..46716189-chr3:46730133..46733448,4	MCF-7	breast:
3	chr3:46729839..46731563-chr3:46733561..46736406,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178038	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11711074	0.89[CHB][hapmap]
rs12496585	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3210183	0.89[CHB][hapmap]
rs34190208	0.88[ASN][1000 genomes]
rs3935248	0.89[CHB][hapmap]
rs4076927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682825	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs55650397	0.89[ASN][1000 genomes]
rs56069285	0.82[AMR][1000 genomes]
rs56670151	0.88[ASN][1000 genomes]
rs59191033	0.91[ASN][1000 genomes]
rs62246183	0.81[AMR][1000 genomes]
rs6442020	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6776464	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6792255	0.85[AMR][1000 genomes]
rs6804514	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7372799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7373358	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73831197	0.92[ASN][1000 genomes]
rs7426833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610936	0.83[ASN][1000 genomes]
rs7615747	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7633016	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634963	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7642448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642783	0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs7649029	0.83[ASN][1000 genomes]
rs7649081	0.82[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs7650366	0.89[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv876739	chr3:46656980-46744966	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv876740	chr3:46656980-46748453	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv876741	chr3:46663372-46763839	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv516623	chr3:46680063-46852679	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	esv1804680	chr3:46704348-46869911	Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv876742	chr3:46705369-46763839	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
11	nsv536555	chr3:46706571-46817963	Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv536556	chr3:46706571-46849443	Genic enhancers Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv536557	chr3:46706571-46853434	Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS 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	35 gene(s)	inside rSNPs	diseases
15	nsv10268	chr3:46707169-46736718	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
16	esv1797503	chr3:46708712-46760713	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
17	nsv876743	chr3:46716523-46753577	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
18	nsv876744	chr3:46716523-46763839	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
19	nsv460525	chr3:46728659-46790397	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
20	nsv590179	chr3:46728659-46790397	Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
21	esv1847964	chr3:46729757-46753976	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46702800-46732400	Weak transcription	Psoas Muscle	Psoas
2	chr3:46703000-46731600	Weak transcription	Hela-S3	cervix
3	chr3:46705400-46732600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:46705400-46734400	Weak transcription	Ovary	ovary
5	chr3:46711400-46731800	Strong transcription	NHEK	skin
6	chr3:46713000-46732000	Weak transcription	Stomach Mucosa	stomach
7	chr3:46715400-46731600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr3:46716000-46732000	Strong transcription	Fetal Intestine Small	intestine
9	chr3:46717400-46733800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:46717800-46733600	Weak transcription	Brain Angular Gyrus	brain
11	chr3:46717800-46734000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:46719200-46732000	Weak transcription	Right Atrium	heart
13	chr3:46720400-46731800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:46720600-46733800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:46721200-46731800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:46723000-46731600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:46724200-46732200	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr3:46725000-46731400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:46725600-46734000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:46725800-46731400	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr3:46726200-46732000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:46727800-46732000	Weak transcription	Liver	Liver
23	chr3:46727800-46732200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:46727800-46732400	Weak transcription	Thymus	Thymus
25	chr3:46727800-46734000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:46728600-46732200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:46729400-46732000	Weak transcription	Placenta	Placenta
28	chr3:46729600-46731400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr3:46729800-46732800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:46730000-46731600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:46730000-46731800	Weak transcription	Colonic Mucosa	Colon
32	chr3:46730000-46731800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr3:46730000-46733800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:46730200-46732600	Weak transcription	Gastric	stomach
35	chr3:46730200-46734400	Weak transcription	Aorta	Aorta
36	chr3:46730400-46731600	Weak transcription	Primary T cells from cord blood	blood
37	chr3:46730400-46731600	Weak transcription	Left Ventricle	heart
38	chr3:46730400-46731600	Weak transcription	HMEC	breast
39	chr3:46730600-46732000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:46730800-46731800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:46730800-46733800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:46731000-46731600	Weak transcription	Esophagus	oesophagus
43	chr3:46731000-46731600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr3:46731000-46731800	Weak transcription	Fetal Intestine Large	intestine
45	chr3:46731000-46732000	Enhancers	Spleen	Spleen
46	chr3:46731000-46732200	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr3:46731000-46732200	Weak transcription	Stomach Smooth Muscle	stomach
48	chr3:46731000-46732600	Weak transcription	Pancreas	Pancrea
49	chr3:46731000-46733600	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr3:46731000-46733600	Enhancers	Lung	lung

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