Variant report

Variant	rs831502
Chromosome Location	chr6:36989391-36989392
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36989173..36991551-chr6:37137394..37139647,3	K562	blood:
2	chr6:36944786..36946944-chr6:36988246..36989759,2	MCF-7	breast:
3	chr6:36989372..36991434-chr6:37069040..37071610,2	MCF-7	breast:
4	chr6:36989098..36990112-chr6:37139646..37140588,5	K562	blood:

Variant related genes	Relation type
ENSG00000137409	Chromatin interaction
ENSG00000137193	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1224487	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1224488	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1224491	0.91[ASN][1000 genomes]
rs1228575	0.93[ASN][1000 genomes]
rs1547571	0.92[CEU][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs1724094	0.91[ASN][1000 genomes]
rs1753301	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2025998	0.93[ASN][1000 genomes]
rs2094575	0.80[ASN][1000 genomes]
rs4317401	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs4711482	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6457974	1.00[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs6457978	0.80[ASN][1000 genomes]
rs6457980	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6924660	0.80[ASN][1000 genomes]
rs6939869	0.81[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7750403	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7750614	0.80[ASN][1000 genomes]
rs7750717	0.80[ASN][1000 genomes]
rs7751821	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs831481	0.81[GIH][hapmap]
rs831484	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs831487	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]
rs831489	0.81[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs831491	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs831497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs831499	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs831500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs831504	0.81[CEU][hapmap];0.95[GIH][hapmap]
rs913499	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs913500	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]
rs9296207	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs9296208	0.80[ASN][1000 genomes]
rs9366927	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs9380637	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
4	nsv885816	chr6:36965099-36999682	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv515488	chr6:36978745-36989587	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	esv3436059	chr6:36986674-36990872	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs831502	FGD2	cis	multi-tissue	Pritchard
rs831502	FGD2	cis	Skin Sun Exposed Lower leg	GTEx
rs831502	FGD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36975600-36989600	Weak transcription	Thymus	Thymus
2	chr6:36983400-36995000	Weak transcription	Lung	lung
3	chr6:36986000-36989600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:36986400-36989400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr6:36986400-36989400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:36986400-36989400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:36986400-36989600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:36986400-36990000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:36986600-36989600	Weak transcription	HSMM	muscle
10	chr6:36986600-36989600	Weak transcription	HUVEC	blood vessel
11	chr6:36986600-36991000	Weak transcription	Stomach Mucosa	stomach
12	chr6:36986600-36992600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr6:36986800-37006600	Weak transcription	Colonic Mucosa	Colon
14	chr6:36987000-36990200	Weak transcription	Adipose Nuclei	Adipose
15	chr6:36987000-36991200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr6:36987000-36991800	Strong transcription	GM12878-XiMat	blood
17	chr6:36987000-36993200	Weak transcription	Placenta	Placenta
18	chr6:36987000-36996800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr6:36987000-36996800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr6:36987200-36989400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr6:36987200-36989400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr6:36987200-36989400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr6:36987200-36989400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:36987200-36989400	Weak transcription	A549	lung
25	chr6:36987200-36989600	Weak transcription	NH-A	brain
26	chr6:36987200-36989600	Weak transcription	NHLF	lung
27	chr6:36987200-36990000	Strong transcription	Spleen	Spleen
28	chr6:36987200-36993800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:36987200-36995000	Strong transcription	Primary B cells from cord blood	blood
30	chr6:36987200-36997200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:36987400-36989400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr6:36987400-36989400	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr6:36987400-36989400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:36987400-36989600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:36987400-36989600	Weak transcription	Hela-S3	cervix
36	chr6:36987400-36989600	Weak transcription	NHEK	skin
37	chr6:36987400-36989800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:36987400-36989800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:36987400-36990000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:36987400-36990000	Weak transcription	Fetal Stomach	stomach
41	chr6:36987600-36989400	Weak transcription	HMEC	breast
42	chr6:36987600-36989800	Weak transcription	Liver	Liver
43	chr6:36987600-36991600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr6:36988200-36990000	Enhancers	H1 Cell Line	embryonic stem cell
45	chr6:36988200-36990000	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr6:36988200-36990000	Enhancers	K562	blood
47	chr6:36988200-36990200	Enhancers	Duodenum Mucosa	Duodenum
48	chr6:36988200-36990200	Enhancers	Esophagus	oesophagus
49	chr6:36988200-36991400	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr6:36988200-36998000	Strong transcription	Primary B cells from peripheral blood	blood

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