Variant report

Variant	rs3900740
Chromosome Location	chr6:86300851-86300852
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:86252970..86255284-chr6:86299533..86301971,2	K562	blood:
2	chr6:86252970..86257934-chr6:86299533..86304034,5	K562	blood:
3	chr6:86299824..86305374-chr6:86350530..86356322,11	MCF-7	breast:
4	chr6:86278096..86280709-chr6:86299065..86302030,2	K562	blood:
5	chr6:86298683..86300956-chr6:86302311..86304856,2	MCF-7	breast:
6	chr6:86300286..86310605-chr6:86384413..86390498,39	K562	blood:
7	chr6:86299850..86302872-chr6:86358961..86362964,3	K562	blood:
8	chr6:86191399..86193392-chr6:86300815..86302853,2	K562	blood:
9	chr6:86300457..86307827-chr6:86347697..86356337,20	K562	blood:
10	chr6:86284643..86286706-chr6:86299863..86303229,3	K562	blood:
11	chr6:86298349..86307534-chr6:86383938..86391964,31	K562	blood:

No data

Variant related genes	Relation type
ENSG00000203875	Chromatin interaction
ENSG00000135316	Chromatin interaction
ENSG00000135317	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs13192070	0.82[ASN][1000 genomes]
rs13194512	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13198956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13202606	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs13208740	1.00[CEU][hapmap];0.84[TSI][hapmap]
rs16876230	0.84[EUR][1000 genomes]
rs16876340	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16876385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16876414	0.82[ASW][hapmap];0.81[CHD][hapmap]
rs16876418	0.82[ASW][hapmap];0.81[CHD][hapmap]
rs1793	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2095483	0.82[ASW][hapmap];0.81[CHD][hapmap]
rs34239697	0.91[EUR][1000 genomes]
rs34898046	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34936540	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35121980	0.87[EUR][1000 genomes]
rs35367106	0.91[EUR][1000 genomes]
rs35694036	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35712823	0.87[EUR][1000 genomes]
rs35988746	0.83[EUR][1000 genomes]
rs36088473	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734442	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];1.00[EUR][1000 genomes]
rs4707206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4707213	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55648312	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55810446	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67493405	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6906121	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6909402	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6909654	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6910641	0.85[EUR][1000 genomes]
rs6915519	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71570763	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71570764	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71570766	0.91[EUR][1000 genomes]
rs7738371	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740830	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742792	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7766863	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7771577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9450302	1.00[YRI][hapmap]

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	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv886334	chr6:86214507-86394403	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
4	esv1792638	chr6:86224053-86336300	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking 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 target site	15 gene(s)	inside rSNPs	diseases
5	esv3351743	chr6:86286282-86308720	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86224200-86302600	Weak transcription	Colonic Mucosa	Colon
2	chr6:86243400-86301400	Weak transcription	Thymus	Thymus
3	chr6:86278200-86302600	Weak transcription	Ovary	ovary
4	chr6:86280000-86301400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr6:86281400-86301600	Weak transcription	Fetal Thymus	thymus
6	chr6:86286600-86302000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:86288200-86301400	Weak transcription	Fetal Heart	heart
8	chr6:86289200-86301000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:86290000-86301000	Weak transcription	Brain Hippocampus Middle	brain
10	chr6:86290200-86301800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:86290400-86301400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:86290400-86302400	Weak transcription	Placenta	Placenta
13	chr6:86290800-86301400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:86290800-86302000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr6:86291000-86302000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:86291000-86302000	Weak transcription	HSMM	muscle
17	chr6:86291000-86302600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr6:86291200-86301000	Weak transcription	Primary T cells from cord blood	blood
19	chr6:86291200-86301200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr6:86291200-86301200	Weak transcription	Hela-S3	cervix
21	chr6:86291200-86301200	Weak transcription	NHEK	skin
22	chr6:86291200-86301400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:86291200-86301800	Weak transcription	HUVEC	blood vessel
24	chr6:86291200-86302600	Weak transcription	Pancreas	Pancrea
25	chr6:86291200-86302600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr6:86291200-86302800	Weak transcription	Gastric	stomach
27	chr6:86292000-86301000	Weak transcription	Primary B cells from cord blood	blood
28	chr6:86292000-86301200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr6:86292000-86301800	Weak transcription	NHDF-Ad	bronchial
30	chr6:86293800-86301000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr6:86294000-86301800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr6:86294600-86301200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:86295000-86301400	Weak transcription	Dnd41	blood
34	chr6:86295600-86301000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:86295600-86301000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:86295800-86301800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:86296000-86301400	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr6:86296600-86301200	Weak transcription	Psoas Muscle	Psoas
39	chr6:86296800-86301200	Weak transcription	Left Ventricle	heart
40	chr6:86296800-86301800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr6:86297000-86301200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr6:86297200-86301800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr6:86297400-86301400	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr6:86297600-86301400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:86297800-86301200	Weak transcription	Fetal Lung	lung
46	chr6:86297800-86301800	Weak transcription	Fetal Kidney	kidney
47	chr6:86297800-86302200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr6:86297800-86302600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr6:86298000-86301000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr6:86298000-86301000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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