Variant report

Variant	rs7169064
Chromosome Location	chr15:31210862-31210863
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:31199252..31201073-chr15:31208786..31211235,2	MCF-7	breast:

Extended variants
information (count: 104 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10163148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519726	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs11070678	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11070718	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs1133642	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs11631543	0.80[ASN][1000 genomes]
rs11638295	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs11852466	0.83[CHB][hapmap]
rs12441318	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs12442333	0.82[CHB][hapmap]
rs12901022	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs12902792	0.92[CHB][hapmap]
rs12904967	0.92[CHB][hapmap]
rs12907055	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911881	0.92[CHB][hapmap]
rs1404468	0.92[CHB][hapmap]
rs1404469	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs1474381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1474382	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1483675	0.92[CHB][hapmap]
rs1524876	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs16956341	0.83[CHB][hapmap]
rs16956362	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs16956366	0.83[CHB][hapmap]
rs16956414	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs16956422	0.83[CHB][hapmap]
rs17815804	0.83[CHD][hapmap]
rs1809484	0.92[CHB][hapmap]
rs1880499	0.92[CHB][hapmap]
rs1880500	0.80[ASN][1000 genomes]
rs2042613	0.92[CHB][hapmap]
rs2113945	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs2113946	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs2272218	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs2272219	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2293314	0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs2293319	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2293320	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2339048	0.80[ASN][1000 genomes]
rs28548813	0.80[ASN][1000 genomes]
rs28693590	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28708881	0.80[ASN][1000 genomes]
rs28721380	0.80[ASN][1000 genomes]
rs2873	0.92[CHB][hapmap];0.85[CHD][hapmap]
rs28881289	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2949566	0.80[ASN][1000 genomes]
rs2949569	0.92[CHB][hapmap]
rs2949570	0.92[CHB][hapmap]
rs2949573	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs2949575	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2949576	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs2949577	0.92[CHB][hapmap]
rs2949578	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs2955783	0.92[CHB][hapmap]
rs2955787	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2955790	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs2955791	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2955796	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs2955798	0.80[ASN][1000 genomes]
rs2959039	0.85[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs2959049	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs35162264	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35497908	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3743231	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs3784588	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs3964705	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs4779796	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4779797	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493358	0.83[CHB][hapmap]
rs71474639	0.81[AFR][1000 genomes]
rs7161812	1.00[CHB][hapmap]
rs7164939	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7165798	0.92[CHB][hapmap]
rs7167980	0.82[ASN][1000 genomes]
rs7170710	0.92[CHB][hapmap]
rs7175951	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs7176351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7178375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7178533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7182143	0.92[CHB][hapmap]
rs798101	0.85[CHB][hapmap]
rs8040345	0.92[CHB][hapmap]
rs8040989	0.92[CHB][hapmap]
rs8041717	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs871312	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs872843	0.83[CHB][hapmap]
rs9806159	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427955	chr15:30467980-31273174	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv916936	chr15:30921917-31337510	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv525795	chr15:30936285-31324531	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv533434	chr15:30938215-31244225	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
7	nsv1046874	chr15:31008133-31294654	Enhancers Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
9	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
10	nsv832951	chr15:31131239-31304469	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv1039037	chr15:31140415-31277268	Strong transcription ZNF genes & repeats Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv542309	chr15:31140415-31277268	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
13	nsv1036018	chr15:31140415-31544888	Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
14	nsv521842	chr15:31140700-31272670	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
15	nsv903834	chr15:31179534-31293774	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	esv33507	chr15:31183324-31471023	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
17	nsv832952	chr15:31204426-31333998	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS 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 miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7169064	GABRG3	cis	parietal	SCAN
rs7169064	MTMR15	Cis_1M	lymphoblastoid	RTeQTL
rs7169064	RP11-932O9.7	cis	Muscle Skeletal	GTEx
rs7169064	SNORD115-35	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31196800-31213000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:31196800-31215000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:31197000-31213400	Weak transcription	Stomach Mucosa	stomach
4	chr15:31197000-31216400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:31197200-31214000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:31197400-31211200	Strong transcription	A549	lung
7	chr15:31197400-31215000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr15:31198200-31224000	Strong transcription	Dnd41	blood
9	chr15:31198400-31213000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr15:31199800-31213400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr15:31200000-31211600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:31200000-31213200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr15:31200200-31211800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:31200200-31213400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr15:31200200-31214400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr15:31200200-31224000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr15:31200400-31213000	Strong transcription	Fetal Muscle Trunk	muscle
18	chr15:31200400-31213400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:31200400-31213800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:31200400-31216200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr15:31200400-31221200	Strong transcription	Placenta	Placenta
22	chr15:31200400-31223200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr15:31200400-31242200	Strong transcription	Primary T cells from cord blood	blood
24	chr15:31200600-31211400	Strong transcription	Fetal Muscle Leg	muscle
25	chr15:31200600-31254800	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr15:31200800-31213400	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:31200800-31213600	Strong transcription	Liver	Liver
28	chr15:31201000-31211200	Strong transcription	Brain Hippocampus Middle	brain
29	chr15:31201200-31211200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:31201200-31211200	Strong transcription	Fetal Brain Female	brain
31	chr15:31201200-31211400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr15:31201200-31224000	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr15:31201200-31241400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:31202000-31212800	Weak transcription	Psoas Muscle	Psoas
35	chr15:31202400-31213800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:31202400-31214000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr15:31202800-31213000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:31203000-31213200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr15:31203200-31211000	Weak transcription	HUVEC	blood vessel
40	chr15:31203200-31212400	Weak transcription	HepG2	liver
41	chr15:31204200-31211400	Strong transcription	Adipose Nuclei	Adipose
42	chr15:31204200-31212800	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr15:31204200-31213000	Strong transcription	Osteobl	bone
44	chr15:31204200-31224000	Strong transcription	Stomach Smooth Muscle	stomach
45	chr15:31204400-31211000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:31204400-31211400	Strong transcription	Fetal Intestine Large	intestine
47	chr15:31204400-31211400	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr15:31204400-31213000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:31204400-31213200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:31204400-31214600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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