Variant report

Variant	rs7076879
Chromosome Location	chr10:90652512-90652513
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:90641054..90643294-chr10:90651464..90653161,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138134	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11202877	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11202880	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11202881	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12245525	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12245668	0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12248501	0.81[AFR][1000 genomes]
rs12254451	1.00[ASW][hapmap];0.84[CHD][hapmap];0.81[LWK][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12262249	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12263461	1.00[ASW][hapmap];0.83[CHD][hapmap];0.81[LWK][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12264141	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12269097	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17113606	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1887025	0.93[EUR][1000 genomes]
rs1926184	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1926185	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1926186	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55885377	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57063754	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57261011	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7075596	1.00[CEU][hapmap]
rs7077019	1.00[ASW][hapmap];0.84[CHD][hapmap];0.81[LWK][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7090604	0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs74147302	0.88[ASN][1000 genomes]
rs74150105	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs755049	1.00[CEU][hapmap]
rs7910708	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7913997	0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs952323	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers 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	66 gene(s)	inside rSNPs	diseases
3	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv831942	chr10:90564697-90730352	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7076879	RERGL	trans	brain	seeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90641000-90653600	Weak transcription	Gastric	stomach
2	chr10:90641400-90658600	Weak transcription	Brain Angular Gyrus	brain
3	chr10:90641600-90653200	Weak transcription	Colonic Mucosa	Colon
4	chr10:90641800-90653800	Weak transcription	Stomach Mucosa	stomach
5	chr10:90641800-90656400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr10:90641800-90661800	Weak transcription	Thymus	Thymus
7	chr10:90642000-90684800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr10:90642000-90686400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr10:90642200-90656600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr10:90642600-90653800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr10:90642800-90656400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr10:90644200-90653400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr10:90646800-90653600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr10:90646800-90656200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr10:90646800-90656800	Weak transcription	Psoas Muscle	Psoas
16	chr10:90647400-90656000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr10:90647400-90675200	Weak transcription	Spleen	Spleen
18	chr10:90647400-90681000	Weak transcription	Aorta	Aorta
19	chr10:90647800-90653600	Enhancers	Osteobl	bone
20	chr10:90648000-90654200	Enhancers	Muscle Satellite Cultured Cells	--
21	chr10:90648000-90656000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr10:90648200-90654000	Weak transcription	Fetal Thymus	thymus
23	chr10:90648200-90654800	Weak transcription	Left Ventricle	heart
24	chr10:90648400-90653200	Weak transcription	Fetal Muscle Leg	muscle
25	chr10:90648400-90653400	Weak transcription	Fetal Intestine Large	intestine
26	chr10:90648400-90653600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr10:90648400-90656200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr10:90648600-90653600	Weak transcription	Fetal Intestine Small	intestine
29	chr10:90648800-90653400	Weak transcription	Adipose Nuclei	Adipose
30	chr10:90649000-90653400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr10:90649200-90653600	Enhancers	NHDF-Ad	bronchial
32	chr10:90649800-90653600	Weak transcription	Primary B cells from cord blood	blood
33	chr10:90649800-90654200	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr10:90649800-90654200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr10:90650000-90653600	Weak transcription	Fetal Lung	lung
36	chr10:90650000-90656200	Weak transcription	Fetal Stomach	stomach
37	chr10:90650200-90653600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr10:90650200-90653600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr10:90650200-90654200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr10:90650400-90653800	Enhancers	HSMM	muscle
41	chr10:90650600-90653600	Weak transcription	Primary T cells from cord blood	blood
42	chr10:90650800-90653400	Weak transcription	Primary B cells from peripheral blood	blood
43	chr10:90650800-90653600	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr10:90650800-90653600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr10:90650800-90653600	Enhancers	NHLF	lung
46	chr10:90650800-90656400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr10:90651000-90652600	Enhancers	GM12878-XiMat	blood
48	chr10:90651000-90655000	Enhancers	A549	lung
49	chr10:90651200-90652600	Enhancers	Hela-S3	cervix
50	chr10:90651600-90652600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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