Variant report

Variant	rs1860934
Chromosome Location	chr7:127481759-127481760
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:127472811..127474462-chr7:127480282..127483012,2	MCF-7	breast:
2	chr7:127481717..127483487-chr7:127483506..127486200,2	MCF-7	breast:

Extended variants
information (count: 118 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10215276	0.92[ASN][1000 genomes]
rs10251423	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10251548	0.96[EUR][1000 genomes]
rs10255861	1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10260037	1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1029927	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1075206	0.85[ASN][1000 genomes]
rs10954163	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11521053	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11971935	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11972774	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11976841	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11976946	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11977012	0.81[ASN][1000 genomes]
rs11977915	0.81[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11980318	0.81[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12531440	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12533846	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12539728	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12540865	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12706818	0.87[AFR][1000 genomes]
rs12706819	0.87[AFR][1000 genomes]
rs12706820	0.87[AFR][1000 genomes]
rs13231367	0.84[AFR][1000 genomes]
rs13236900	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13237048	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13246200	0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs1362268	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1362897	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs141450	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1419969	0.87[ASN][1000 genomes]
rs16885524	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17151241	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17151270	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17151466	0.82[ASW][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes]
rs17676986	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17716738	0.81[ASN][1000 genomes]
rs17718395	0.92[ASN][1000 genomes]
rs1881084	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2014583	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2016786	0.93[EUR][1000 genomes]
rs2043982	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2119452	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2119453	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2141259	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2402866	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2402867	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2402870	0.94[EUR][1000 genomes]
rs325440	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs325442	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325444	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325445	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325446	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325447	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325451	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35121681	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35176520	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35940771	0.94[EUR][1000 genomes]
rs35971861	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3757767	0.83[ASN][1000 genomes]
rs3779529	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3779530	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808057	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs3808058	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3808073	1.00[JPT][hapmap]
rs3808084	0.83[ASN][1000 genomes]
rs3808087	0.87[ASN][1000 genomes]
rs3808092	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3808093	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3808095	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3808097	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3808105	0.81[ASN][1000 genomes]
rs3808106	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3808107	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3808112	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3824000	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs41464647	0.81[ASW][hapmap]
rs4728077	0.81[ASN][1000 genomes]
rs4731376	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4731378	0.93[EUR][1000 genomes]
rs55694225	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56306023	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58583807	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6467145	0.93[EUR][1000 genomes]
rs67827668	0.87[AFR][1000 genomes]
rs6948493	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6961381	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6963455	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6963614	1.00[JPT][hapmap]
rs6968199	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6969880	0.98[EUR][1000 genomes]
rs712712	0.87[EUR][1000 genomes]
rs712716	0.96[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs73234861	0.81[ASN][1000 genomes]
rs73234862	0.81[ASN][1000 genomes]
rs73234880	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73234882	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73234897	0.92[ASN][1000 genomes]
rs741599	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs759056	0.81[ASN][1000 genomes]
rs759843	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7785050	0.98[EUR][1000 genomes]
rs7786041	0.92[ASN][1000 genomes]
rs7797663	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7799882	0.94[EUR][1000 genomes]
rs7810024	0.87[AFR][1000 genomes]
rs887745	1.00[JPT][hapmap]
rs917831	1.00[JPT][hapmap]
rs917832	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs918793	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs972088	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs972089	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs972090	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv831123	chr7:127289511-127510396	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv526535	chr7:127445594-127623840	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1860934	SND1	cis	parietal	SCAN
rs1860934	GPR37	cis	cerebellum	SCAN
rs1860934	HYAL4	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127448400-127484800	Weak transcription	Aorta	Aorta
2	chr7:127449000-127484200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr7:127457000-127497800	Weak transcription	Gastric	stomach
4	chr7:127461000-127484400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:127461000-127495600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr7:127461000-127497600	Weak transcription	Fetal Stomach	stomach
7	chr7:127461600-127485600	Weak transcription	HSMMtube	muscle
8	chr7:127463600-127482800	Weak transcription	Small Intestine	intestine
9	chr7:127465000-127483200	Weak transcription	HepG2	liver
10	chr7:127469400-127488800	Weak transcription	Thymus	Thymus
11	chr7:127470200-127484400	Weak transcription	Fetal Heart	heart
12	chr7:127471800-127484200	Weak transcription	Left Ventricle	heart
13	chr7:127471800-127495600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr7:127472200-127484000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr7:127472800-127483800	Weak transcription	Brain Substantia Nigra	brain
16	chr7:127473800-127482800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr7:127473800-127482800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr7:127474000-127484400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr7:127474000-127495800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr7:127474200-127485200	Weak transcription	Hela-S3	cervix
21	chr7:127474200-127490400	Weak transcription	NHLF	lung
22	chr7:127474400-127486800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr7:127474600-127482800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr7:127474600-127484200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr7:127476200-127487600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr7:127476400-127483200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr7:127476600-127496400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr7:127477400-127483600	Weak transcription	HSMM	muscle
29	chr7:127477600-127484600	Weak transcription	Fetal Kidney	kidney
30	chr7:127477800-127482800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr7:127477800-127484400	Weak transcription	NH-A	brain
32	chr7:127477800-127493200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr7:127478200-127482200	Weak transcription	Liver	Liver
34	chr7:127478200-127482400	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr7:127478200-127482600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr7:127478200-127482800	Weak transcription	NHEK	skin
37	chr7:127478200-127483000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr7:127478200-127483000	Weak transcription	HMEC	breast
39	chr7:127478200-127483200	Weak transcription	Primary T cells from cord blood	blood
40	chr7:127478200-127483200	Weak transcription	Dnd41	blood
41	chr7:127478200-127483600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr7:127478200-127483800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr7:127478200-127484200	Weak transcription	Psoas Muscle	Psoas
44	chr7:127478200-127484400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr7:127478200-127484600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr7:127478200-127487800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr7:127478400-127482200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr7:127478400-127482200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr7:127478400-127483200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr7:127478400-127483400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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