Variant report

Variant	rs3950186
Chromosome Location	chr6:11811314-11811315
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:11811052..11812674-chr6:11998297..11999883,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HIVEP1-4	chr6:11811076-11811481	XLOC_005171

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1014972	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947579	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1569731	0.88[ASN][1000 genomes]
rs1569735	0.89[ASN][1000 genomes]
rs16871833	0.95[CEU][hapmap]
rs1883324	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1883325	0.95[CEU][hapmap]
rs1883326	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2143715	0.95[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs2179742	1.00[CEU][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4308554	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4310046	0.88[ASN][1000 genomes]
rs4404760	0.95[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs4557506	0.88[ASN][1000 genomes]
rs4634440	0.89[ASN][1000 genomes]
rs6899747	0.90[ASN][1000 genomes]
rs6910363	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6936286	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6941812	0.95[CEU][hapmap]
rs6942235	0.95[CEU][hapmap]
rs7739256	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743245	0.95[CEU][hapmap];0.84[CHD][hapmap]
rs7766152	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9470184	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470216	0.86[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs978565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][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	esv2758036	chr6:11679753-11822351	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759407	chr6:11679753-11822351	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Anxiety and major depressive disorder	24047446	GWAS catalog

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11807600-11816400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr6:11808000-11814400	Weak transcription	Fetal Thymus	thymus
3	chr6:11809200-11811400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr6:11809600-11811400	Enhancers	Muscle Satellite Cultured Cells	--
5	chr6:11809600-11811400	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr6:11809800-11811400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:11809800-11811400	Enhancers	Adipose Nuclei	Adipose
8	chr6:11809800-11811400	Enhancers	Ovary	ovary
9	chr6:11809800-11811400	Enhancers	Stomach Smooth Muscle	stomach
10	chr6:11809800-11811600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:11809800-11811800	Enhancers	Fetal Muscle Leg	muscle
12	chr6:11809800-11812000	Enhancers	Fetal Lung	lung
13	chr6:11809800-11812000	Enhancers	Stomach Mucosa	stomach
14	chr6:11809800-11812200	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr6:11809800-11812600	Enhancers	Fetal Heart	heart
16	chr6:11810000-11811400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:11810000-11811400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:11810200-11811400	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr6:11810200-11811400	Enhancers	Fetal Kidney	kidney
20	chr6:11810200-11811400	Enhancers	K562	blood
21	chr6:11810200-11811800	Enhancers	Fetal Muscle Trunk	muscle
22	chr6:11810400-11811400	Enhancers	Gastric	stomach
23	chr6:11810400-11811400	Enhancers	Left Ventricle	heart
24	chr6:11810400-11811400	Enhancers	Right Atrium	heart
25	chr6:11810400-11811600	Enhancers	Brain Cingulate Gyrus	brain
26	chr6:11810400-11811600	Enhancers	Brain Hippocampus Middle	brain
27	chr6:11810400-11811800	Enhancers	Brain Angular Gyrus	brain
28	chr6:11810400-11812000	Enhancers	Fetal Brain Male	brain
29	chr6:11810600-11811400	Weak transcription	Spleen	Spleen
30	chr6:11810600-11812200	Enhancers	Brain Germinal Matrix	brain
31	chr6:11810600-11814000	Weak transcription	Fetal Intestine Small	intestine
32	chr6:11810800-11811400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:11810800-11813400	Weak transcription	Fetal Intestine Large	intestine
34	chr6:11810800-11814800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:11810800-11815000	Weak transcription	NHEK	skin
36	chr6:11810800-11815200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:11810800-11815400	Weak transcription	Fetal Stomach	stomach
38	chr6:11810800-11815600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:11811000-11811400	Flanking Active TSS	Brain Anterior Caudate	brain
40	chr6:11811000-11811400	Enhancers	A549	lung
41	chr6:11811000-11811400	Enhancers	HSMM	muscle
42	chr6:11811000-11811600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:11811000-11811600	Enhancers	Hela-S3	cervix
44	chr6:11811000-11811600	Enhancers	Osteobl	bone
45	chr6:11811000-11814400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr6:11811000-11814400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr6:11811200-11811400	Flanking Active TSS	HSMMtube	muscle
48	chr6:11811200-11811600	Active TSS	Fetal Brain Female	brain
49	chr6:11811200-11812000	Weak transcription	GM12878-XiMat	blood
50	chr6:11811200-11815000	Weak transcription	HMEC	breast

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