Variant report

Variant	rs831487
Chromosome Location	chr6:37001227-37001228
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	chr6:36996690..36999564-chr6:37000125..37002261,3	MCF-7	breast:
2	chr6:36999943..37003215-chr6:37137144..37140064,3	MCF-7	breast:
3	chr6:36998448..37001378-chr6:37003343..37005292,2	K562	blood:
4	chr6:36990312..36994052-chr6:36999183..37001742,4	MCF-7	breast:
5	chr6:36999933..37002459-chr6:37159726..37162067,2	K562	blood:
6	chr6:36998830..37003518-chr6:37005337..37008054,4	K562	blood:
7	chr6:36996704..36998294-chr6:37000427..37002099,2	K562	blood:
8	chr6:36993041..37002133-chr6:37135266..37141596,21	K562	blood:
9	chr6:36997224..37001862-chr6:37173680..37176936,6	K562	blood:
10	chr6:36998546..37003214-chr6:37136049..37138990,5	K562	blood:
11	chr6:37001172..37003656-chr6:37177575..37179330,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000137193	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1224487	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1224488	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1224491	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1228575	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547571	0.83[GIH][hapmap]
rs1724094	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1753300	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1753301	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025998	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094575	0.86[ASN][1000 genomes]
rs2149336	0.83[ASN][1000 genomes]
rs4317401	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711482	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457974	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457976	0.85[ASN][1000 genomes]
rs6457978	0.86[ASN][1000 genomes]
rs6457979	0.82[ASN][1000 genomes]
rs6457980	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs6924660	0.86[ASN][1000 genomes]
rs6939869	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748291	0.85[ASN][1000 genomes]
rs7750403	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7750614	0.86[ASN][1000 genomes]
rs7750717	0.86[ASN][1000 genomes]
rs7751821	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7770544	0.83[ASN][1000 genomes]
rs831481	0.84[GIH][hapmap]
rs831484	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs831489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs831491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs831497	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs831499	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs831500	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs831502	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs831504	0.88[GIH][hapmap]
rs865550	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs913499	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs913500	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs913501	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9296207	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs9296208	0.86[ASN][1000 genomes]
rs9366927	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9380637	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394401	0.85[ASN][1000 genomes]
rs9394402	0.81[ASN][1000 genomes]
rs9394403	0.81[ASN][1000 genomes]
rs9462258	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv518386	chr6:36942746-37037670	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs831487	FGD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36986800-37006600	Weak transcription	Colonic Mucosa	Colon
2	chr6:36988600-37006600	Weak transcription	Fetal Intestine Small	intestine
3	chr6:36990200-37006600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr6:36991000-37001600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr6:36992600-37005800	Weak transcription	Liver	Liver
6	chr6:36992800-37006600	Weak transcription	Gastric	stomach
7	chr6:36993800-37018200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:36995800-37006600	Weak transcription	Lung	lung
9	chr6:36997400-37002400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:36997400-37013800	Weak transcription	Esophagus	oesophagus
11	chr6:36997600-37001800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr6:36998800-37001600	Strong transcription	Primary B cells from cord blood	blood
13	chr6:36998800-37006200	Weak transcription	Adipose Nuclei	Adipose
14	chr6:36999000-37001600	Strong transcription	Primary B cells from peripheral blood	blood
15	chr6:36999400-37001600	Strong transcription	Spleen	Spleen
16	chr6:36999600-37001600	Strong transcription	GM12878-XiMat	blood
17	chr6:37000200-37002600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:37000400-37015200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:37000600-37001600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr6:37000600-37002600	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr6:37000800-37002400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:37001000-37002600	Enhancers	K562	blood
23	chr6:37001200-37001600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:37001200-37001600	Flanking Bivalent TSS/Enh	HepG2	liver
25	chr6:37001200-37002000	Genic enhancers	Primary monocytes fromperipheralblood	blood
26	chr6:37001200-37002000	Enhancers	Primary T cells fromperipheralblood	blood
27	chr6:37001200-37002000	Enhancers	Pancreas	Pancrea
28	chr6:37001200-37002200	Genic enhancers	Monocytes-CD14+_RO01746	blood
29	chr6:37001200-37002600	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr6:37001200-37003000	Enhancers	Primary neutrophils fromperipheralblood	blood

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