Variant report

Variant	rs7950602
Chromosome Location	chr11:18603332-18603333
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:18599363..18605712-chr11:18606522..18612149,6	MCF-7	breast:
2	chr11:18597269..18603847-chr11:18605648..18613112,11	MCF-7	breast:
3	chr11:18602318..18604842-chr11:18617296..18619257,2	K562	blood:
4	chr11:18602082..18603757-chr11:18635005..18637571,2	MCF-7	breast:
5	chr11:18601940..18604389-chr11:18617103..18619378,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256282	Chromatin interaction
ENSG00000151116	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10219166	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10500835	0.90[TSI][hapmap]
rs10832938	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10832942	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832943	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10832945	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024670	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11024671	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11024674	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11024675	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11024677	0.85[TSI][hapmap]
rs11024678	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11024679	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11024683	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11024685	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11024688	0.85[TSI][hapmap]
rs11024689	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11024695	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11024696	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11024706	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024716	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11024723	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024724	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11024727	0.81[TSI][hapmap]
rs12049851	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12049909	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12049912	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12222154	0.90[TSI][hapmap]
rs12222210	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12223858	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12223887	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12225461	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12225463	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12289223	0.90[TSI][hapmap]
rs12290527	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12418726	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12419360	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12419592	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12420702	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12420882	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421881	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12574333	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12575390	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12577874	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12803251	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1550869	0.81[ASN][1000 genomes]
rs16914838	0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16935504	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16935575	0.90[TSI][hapmap]
rs1972960	0.81[ASN][1000 genomes]
rs2271080	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279900	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2279902	0.85[TSI][hapmap]
rs2305166	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28607050	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3781639	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3781640	0.85[TSI][hapmap]
rs4436523	0.85[TSI][hapmap]
rs4757673	0.81[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs55964013	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55999230	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56097703	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56151250	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56151849	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56411332	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59032896	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61882885	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61882887	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61882903	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61882904	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61884677	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7108487	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7109314	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7109496	0.82[YRI][hapmap]
rs7130163	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72871737	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72876745	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9633899	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats 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 miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv1042155	chr11:18435855-18697576	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv1046886	chr11:18547568-18781448	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv540956	chr11:18547568-18781448	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7950602	TSG101	cis	lymphoblastoid	seeQTL
rs7950602	NUCB2	cis	cerebellum	SCAN
rs7950602	TSG101	Cis_1M	lymphoblastoid	RTeQTL
rs7950602	LDHC	cis	parietal	SCAN
rs7950602	UEVLD	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18549600-18608600	Weak transcription	Fetal Heart	heart
2	chr11:18549600-18609000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:18549600-18609000	Weak transcription	Fetal Brain Male	brain
4	chr11:18563800-18608800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:18565200-18609400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:18574400-18609400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:18575000-18609200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr11:18575200-18609200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr11:18578000-18608800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:18578000-18609000	Weak transcription	Right Ventricle	heart
11	chr11:18578200-18609000	Weak transcription	Primary T cells from cord blood	blood
12	chr11:18578400-18609000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr11:18578600-18608400	Weak transcription	Psoas Muscle	Psoas
14	chr11:18580000-18608600	Weak transcription	Hela-S3	cervix
15	chr11:18580200-18608600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr11:18581000-18609000	Weak transcription	Pancreas	Pancrea
17	chr11:18583000-18608200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr11:18583000-18609400	Weak transcription	Esophagus	oesophagus
19	chr11:18583200-18604600	Weak transcription	Gastric	stomach
20	chr11:18584200-18608000	Weak transcription	Small Intestine	intestine
21	chr11:18584400-18609800	Weak transcription	Spleen	Spleen
22	chr11:18585800-18608600	Weak transcription	Fetal Brain Female	brain
23	chr11:18586400-18609000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr11:18588200-18608800	Weak transcription	Fetal Kidney	kidney
25	chr11:18591800-18608800	Weak transcription	NHEK	skin
26	chr11:18592200-18609000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:18592200-18609400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr11:18593000-18608200	Weak transcription	Brain Germinal Matrix	brain
29	chr11:18593400-18608600	Weak transcription	Dnd41	blood
30	chr11:18593600-18609400	Weak transcription	Aorta	Aorta
31	chr11:18594800-18608800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr11:18594800-18609000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr11:18595000-18608600	Weak transcription	Brain Angular Gyrus	brain
34	chr11:18595000-18609000	Weak transcription	Primary B cells from cord blood	blood
35	chr11:18595200-18609200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr11:18595800-18608800	Weak transcription	NHLF	lung
37	chr11:18596400-18608400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr11:18597200-18608000	Weak transcription	Brain Hippocampus Middle	brain
39	chr11:18597200-18608800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr11:18597200-18609000	Weak transcription	Fetal Thymus	thymus
41	chr11:18597400-18608400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr11:18597400-18608600	Weak transcription	HMEC	breast
43	chr11:18597600-18608600	Weak transcription	Brain Anterior Caudate	brain
44	chr11:18597600-18608800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr11:18597600-18608800	Weak transcription	Brain Substantia Nigra	brain
46	chr11:18597600-18608800	Weak transcription	HUVEC	blood vessel
47	chr11:18598400-18608800	Weak transcription	Thymus	Thymus
48	chr11:18598800-18605800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr11:18598800-18608400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr11:18599000-18608800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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