Variant report

Variant	rs6979423
Chromosome Location	chr7:38891290-38891291
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:38884593..38886823-chr7:38890906..38893182,2	MCF-7	breast:
2	chr7:38889563..38891670-chr7:38895298..38897406,2	K562	blood:
3	chr7:38882709..38885356-chr7:38890864..38893223,2	K562	blood:
4	chr7:38887343..38889713-chr7:38889792..38892384,2	MCF-7	breast:

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10085487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1012976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10224856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10225415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10225550	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10229055	1.00[CHB][hapmap]
rs10242407	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10254354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10254873	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10266279	0.89[EUR][1000 genomes]
rs10270427	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10275873	1.00[CHB][hapmap]
rs10951574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10951575	1.00[JPT][hapmap]
rs11983387	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12701653	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12701656	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12701657	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12701661	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12701671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13224619	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13224857	1.00[ASN][1000 genomes]
rs13229445	1.00[ASN][1000 genomes]
rs13230196	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13231372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13235997	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13236092	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13238093	1.00[AFR][1000 genomes]
rs1558111	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs17240051	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17680342	0.82[CEU][hapmap]
rs2040878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2058073	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2079546	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2107742	1.00[JPT][hapmap]
rs2108508	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2189854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2190667	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2190668	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2190670	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2214667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2214668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2215032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2286089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2286093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2286101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2286103	1.00[JPT][hapmap]
rs2392599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2392608	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs2392610	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34349310	1.00[AFR][1000 genomes]
rs34358406	1.00[AFR][1000 genomes]
rs34621392	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34886315	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34997080	1.00[ASN][1000 genomes]
rs35220172	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35400125	1.00[ASN][1000 genomes]
rs35667896	1.00[AFR][1000 genomes]
rs35816439	1.00[ASN][1000 genomes]
rs35843038	1.00[ASN][1000 genomes]
rs36004953	1.00[AFR][1000 genomes]
rs36114334	1.00[AFR][1000 genomes]
rs36121032	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs37472	1.00[JPT][hapmap]
rs37473	1.00[JPT][hapmap]
rs37476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs37477	1.00[JPT][hapmap]
rs37478	1.00[JPT][hapmap]
rs37479	1.00[JPT][hapmap]
rs40445	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4720300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4720302	1.00[JPT][hapmap]
rs4723780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4723781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4723784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4723786	1.00[JPT][hapmap]
rs4723787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4723802	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4723804	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462866	1.00[JPT][hapmap]
rs6462871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6462873	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6462874	0.91[EUR][1000 genomes]
rs6947695	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6949958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6951429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6960945	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963090	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6964985	0.91[EUR][1000 genomes]
rs6967384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6971632	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6974764	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6975410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6976302	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976579	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976580	1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs71548633	1.00[AFR][1000 genomes]
rs73370730	1.00[ASN][1000 genomes]
rs757685	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs758087	1.00[JPT][hapmap]
rs758088	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782140	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782277	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783723	0.91[EUR][1000 genomes]
rs7784065	0.91[EUR][1000 genomes]
rs7784609	0.91[EUR][1000 genomes]
rs7787423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7789864	0.91[EUR][1000 genomes]
rs7790054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7793250	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs7799887	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs7802052	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7803488	1.00[CHB][hapmap]
rs9638945	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs976350	1.00[JPT][hapmap]
rs976352	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9886108	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032637	chr7:38832627-38902723	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv887966	chr7:38835035-38933942	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6979423	VPS41	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38835600-38900800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:38858600-38901600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr7:38858800-38907600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:38859000-38895200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr7:38859800-38900800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr7:38860600-38900200	Weak transcription	Fetal Intestine Large	intestine
7	chr7:38867400-38905200	Weak transcription	Left Ventricle	heart
8	chr7:38870000-38895600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:38870200-38895600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr7:38871400-38905800	Weak transcription	Aorta	Aorta
11	chr7:38871400-38920000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:38871600-38906000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr7:38873000-38907600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr7:38873200-38919200	Weak transcription	Pancreas	Pancrea
15	chr7:38875800-38897400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr7:38876400-38906200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr7:38877000-38895600	Weak transcription	Spleen	Spleen
18	chr7:38877200-38900800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr7:38877200-38901200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr7:38877400-38896200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr7:38879800-38891800	Weak transcription	Right Atrium	heart
22	chr7:38879800-38938000	Weak transcription	Right Ventricle	heart
23	chr7:38880200-38897600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr7:38880600-38900600	Weak transcription	Adipose Nuclei	Adipose
25	chr7:38880800-38905600	Weak transcription	Fetal Muscle Leg	muscle
26	chr7:38881200-38895000	Weak transcription	GM12878-XiMat	blood
27	chr7:38881200-38898000	Weak transcription	HSMMtube	muscle
28	chr7:38881200-38898000	Weak transcription	NHLF	lung
29	chr7:38881200-38900000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr7:38881200-38907600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr7:38881200-38919200	Weak transcription	Psoas Muscle	Psoas
32	chr7:38881400-38898000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr7:38883400-38907600	Weak transcription	Esophagus	oesophagus
34	chr7:38884600-38905600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr7:38885000-38893800	Weak transcription	Small Intestine	intestine
36	chr7:38885000-38900800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr7:38885800-38897200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr7:38886200-38893000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:38886200-38901400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr7:38886200-38947800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr7:38886400-38898000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr7:38886400-38907400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr7:38886400-38907400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr7:38886400-38907600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr7:38886600-38901200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr7:38886600-38907200	Weak transcription	Colon Smooth Muscle	Colon
47	chr7:38886800-38897600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr7:38886800-38898000	Weak transcription	Brain Substantia Nigra	brain
49	chr7:38887200-38899800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr7:38887200-38906600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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