Variant report

Variant	rs831481
Chromosome Location	chr6:37002182-37002183
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 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	chr6:36999933..37002459-chr6:37159726..37162067,2	K562	blood:
4	chr6:36998830..37003518-chr6:37005337..37008054,4	K562	blood:
5	chr6:37001432..37004372-chr6:37005152..37007455,4	K562	blood:
6	chr6:36998393..36999918-chr6:37001477..37003042,2	K562	blood:
7	chr6:36998546..37003214-chr6:37136049..37138990,5	K562	blood:
8	chr6:37001172..37003656-chr6:37177575..37179330,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000137193	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10947654	0.89[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10947655	0.96[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1224492	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1224493	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1724092	0.87[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1724093	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1753297	0.89[ASW][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1753299	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2692878	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2692879	0.82[ASN][1000 genomes]
rs6457968	0.96[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6457969	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6457970	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6917839	0.87[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6922840	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6939869	0.84[GIH][hapmap]
rs6940573	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6940597	0.91[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7751883	0.91[CHB][hapmap];0.86[CHD][hapmap]
rs831482	0.87[CHB][hapmap];0.87[JPT][hapmap];0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs831483	0.89[ASW][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs831485	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs831486	0.87[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.83[LWK][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs831487	0.84[GIH][hapmap]
rs831488	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs831489	0.84[GIH][hapmap]
rs831490	0.87[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs831497	0.84[GIH][hapmap]
rs831500	0.81[GIH][hapmap]
rs831502	0.81[GIH][hapmap]
rs831504	0.86[GIH][hapmap]
rs831508	0.87[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs864396	0.89[ASW][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs864590	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs913502	0.80[ASN][1000 genomes]
rs9357233	0.91[CHB][hapmap]
rs9380636	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9462254	0.82[AFR][1000 genomes]
rs9765964	0.96[AFR][1000 genomes];0.85[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs831481	FGD2	cis	multi-tissue	Pritchard
rs831481	PIM1	cis	lymphoblastoid	seeQTL

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	chr6:36992600-37005800	Weak transcription	Liver	Liver
5	chr6:36992800-37006600	Weak transcription	Gastric	stomach
6	chr6:36993800-37018200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:36995800-37006600	Weak transcription	Lung	lung
8	chr6:36997400-37002400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:36997400-37013800	Weak transcription	Esophagus	oesophagus
10	chr6:36998800-37006200	Weak transcription	Adipose Nuclei	Adipose
11	chr6:37000200-37002600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:37000400-37015200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:37000600-37002600	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr6:37000800-37002400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:37001000-37002600	Enhancers	K562	blood
16	chr6:37001200-37002200	Genic enhancers	Monocytes-CD14+_RO01746	blood
17	chr6:37001200-37002600	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr6:37001200-37003000	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr6:37001400-37002600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:37001600-37002400	Genic enhancers	Primary B cells from cord blood	blood
21	chr6:37001600-37003000	Genic enhancers	Primary B cells from peripheral blood	blood
22	chr6:37001600-37003200	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr6:37001600-37007600	Weak transcription	GM12878-XiMat	blood
24	chr6:37001800-37002200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr6:37002000-37002400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:37002000-37005400	Weak transcription	Spleen	Spleen
27	chr6:37002000-37006000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:37002000-37006000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr6:37002000-37006800	Weak transcription	Pancreas	Pancrea
30	chr6:37002000-37009200	Weak transcription	Primary T cells fromperipheralblood	blood

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