Variant report

Variant	rs6860934
Chromosome Location	chr5:96001842-96001843
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:96001057..96002966-chr5:96015196..96017728,2	K562	blood:
2	chr5:96000243..96001872-chr5:96034533..96037143,2	MCF-7	breast:
3	chr5:96001062..96004442-chr5:96008712..96011350,3	MCF-7	breast:
4	chr5:95994913..95997156-chr5:96000541..96002076,2	MCF-7	breast:
5	chr5:96000044..96002037-chr5:96005700..96007687,2	MCF-7	breast:
6	chr5:96001506..96003727-chr5:96014793..96017258,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10045215	0.87[ASN][1000 genomes]
rs10067766	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10075736	0.87[ASN][1000 genomes]
rs1421911	0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs151835	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs151904	1.00[JPT][hapmap]
rs152005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs152014	0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs152017	0.89[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs152020	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2351245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs246109	0.81[ASN][1000 genomes]
rs26482	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs26483	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs26484	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs26485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs26503	1.00[JPT][hapmap]
rs26504	1.00[JPT][hapmap]
rs28040	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28093	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs28104	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs31248	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs31249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs31250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4267886	0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4590196	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6556937	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6897588	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7704167	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7705824	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7733671	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.96[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	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6860934	CTC-506B8.1	cis	Nerve Tibial	GTEx
rs6860934	CAST	cis	Liver	GTEx
rs6860934	CAST	cis	Esophagus Muscularis	GTEx
rs6860934	CAST	cis	Adipose Subcutaneous	GTEx
rs6860934	CAST	cis	multi-tissue	Pritchard
rs6860934	CAST	cis	lung	GTEx
rs6860934	CAST	cis	Nerve Tibial	GTEx
rs6860934	CTC-506B8.1	cis	Adipose Subcutaneous	GTEx
rs6860934	CAST	cis	Whole Blood	GTEx
rs6860934	CTC-506B8.1	cis	Whole Blood	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95999400-96002000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:95999400-96002600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:95999400-96002800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr5:95999400-96005000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:95999400-96018200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr5:95999400-96038000	Weak transcription	Fetal Stomach	stomach
7	chr5:95999600-96002000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:95999600-96002000	Weak transcription	Colonic Mucosa	Colon
9	chr5:95999600-96002000	Weak transcription	Psoas Muscle	Psoas
10	chr5:95999600-96002200	Weak transcription	Esophagus	oesophagus
11	chr5:95999600-96003800	Weak transcription	Fetal Kidney	kidney
12	chr5:95999600-96003800	Weak transcription	Gastric	stomach
13	chr5:95999600-96004400	Weak transcription	Right Atrium	heart
14	chr5:95999600-96004600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:95999600-96004600	Weak transcription	Lung	lung
16	chr5:95999600-96004600	Weak transcription	Ovary	ovary
17	chr5:95999600-96006800	Weak transcription	Right Ventricle	heart
18	chr5:95999600-96006800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr5:95999600-96006800	Weak transcription	Spleen	Spleen
20	chr5:95999600-96012400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:95999600-96016600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:95999600-96016600	Weak transcription	HSMMtube	muscle
23	chr5:95999600-96026000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:95999600-96028200	Weak transcription	Aorta	Aorta
25	chr5:95999600-96037800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr5:95999600-96038000	Weak transcription	Fetal Lung	lung
27	chr5:95999800-96004400	Weak transcription	GM12878-XiMat	blood
28	chr5:95999800-96010800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr5:95999800-96022800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr5:95999800-96024600	Weak transcription	Fetal Heart	heart
31	chr5:96000000-96005000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:96000400-96002000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr5:96000400-96003800	Enhancers	Duodenum Mucosa	Duodenum
34	chr5:96000400-96004400	Weak transcription	Left Ventricle	heart
35	chr5:96000400-96005200	Weak transcription	Primary B cells from cord blood	blood
36	chr5:96000400-96005400	Weak transcription	Pancreas	Pancrea
37	chr5:96000400-96007600	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr5:96000400-96010800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr5:96000400-96013400	Weak transcription	Placenta	Placenta
40	chr5:96000400-96016400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr5:96000400-96018400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr5:96000600-96002400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:96000600-96004000	Weak transcription	HepG2	liver
44	chr5:96000600-96010800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr5:96000600-96011000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr5:96000600-96013200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr5:96000800-96002400	Weak transcription	A549	lung
48	chr5:96000800-96003800	Weak transcription	Liver	Liver
49	chr5:96000800-96005000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr5:96000800-96007000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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