Variant report

Variant	rs6570963
Chromosome Location	chr6:149691355-149691356
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149691320..149693840-chr6:149697416..149698951,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11155639	0.81[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs11155641	0.96[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11155644	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219868	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1446556	0.81[CEU][hapmap];0.93[CHB][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs1626823	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1900300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs237009	0.80[EUR][1000 genomes]
rs237010	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs237012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs237016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs237018	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs237019	0.83[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs237024	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs237025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs237026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs237028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs237029	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs237034	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs237035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs366905	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs372205	0.88[CEU][hapmap];0.89[TSI][hapmap]
rs394563	0.84[GIH][hapmap]
rs438852	0.84[GIH][hapmap]
rs4895787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6570964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906384	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922130	0.80[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6942381	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752555	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7753269	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs805026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[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	nsv1024106	chr6:149622349-149745053	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv522875	chr6:149643709-149762537	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6570963	SHPRH	cis	cerebellum	SCAN
rs6570963	LRP11	cis	parietal	SCAN
rs6570963	RAET1E	cis	cerebellum	SCAN
rs6570963	SUMO4	cis	cerebellum	SCAN
rs6570963	LRP11	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149656800-149694400	Weak transcription	Placenta	Placenta
2	chr6:149658000-149695400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:149658800-149692400	Weak transcription	Fetal Kidney	kidney
4	chr6:149659200-149691400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr6:149660400-149699200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:149662200-149694800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:149664000-149694400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr6:149674600-149691800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:149674600-149699200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:149674600-149699200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:149674600-149699200	Weak transcription	Fetal Intestine Large	intestine
12	chr6:149677400-149692400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:149677800-149699200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr6:149680000-149692400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:149680000-149699200	Weak transcription	Fetal Brain Male	brain
16	chr6:149681000-149694800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:149681200-149699200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:149681600-149691600	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr6:149681800-149695000	Weak transcription	Adipose Nuclei	Adipose
20	chr6:149681800-149699200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:149682600-149699200	Weak transcription	Esophagus	oesophagus
22	chr6:149682600-149699200	Weak transcription	Spleen	Spleen
23	chr6:149682600-149709200	Weak transcription	Psoas Muscle	Psoas
24	chr6:149682800-149692400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:149682800-149699200	Weak transcription	Lung	lung
26	chr6:149683400-149698800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:149683600-149692400	Weak transcription	NH-A	brain
28	chr6:149683600-149699400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:149684400-149698800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:149684600-149699200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:149685000-149694000	Weak transcription	NHEK	skin
32	chr6:149685200-149694800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr6:149685200-149699200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr6:149685200-149699400	Weak transcription	HMEC	breast
35	chr6:149685400-149692000	Weak transcription	Small Intestine	intestine
36	chr6:149685400-149692400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr6:149685600-149699200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr6:149685600-149699200	Weak transcription	Gastric	stomach
39	chr6:149685600-149699400	Weak transcription	Brain Angular Gyrus	brain
40	chr6:149685600-149699400	Weak transcription	Fetal Intestine Small	intestine
41	chr6:149685800-149691800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:149685800-149692000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr6:149685800-149692000	Weak transcription	Pancreas	Pancrea
44	chr6:149685800-149692400	Weak transcription	Ovary	ovary
45	chr6:149685800-149699200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:149685800-149699200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr6:149685800-149699200	Weak transcription	Fetal Stomach	stomach
48	chr6:149685800-149699200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr6:149685800-149699600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr6:149686000-149692400	Weak transcription	HepG2	liver

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