Variant report

Variant	rs2177381
Chromosome Location	chr6:34977375-34977376
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:34976217..34981550-chr6:34982184..34986897,6	K562	blood:
2	chr6:34976709..34980316-chr6:34984375..34986897,3	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1051115	0.85[YRI][hapmap]
rs10807144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10807145	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10947536	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12212217	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12661991	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13191009	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13191889	0.81[JPT][hapmap]
rs13219624	0.94[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];0.96[YRI][hapmap]
rs1535001	0.95[GIH][hapmap]
rs1555107	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs16896390	0.82[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs1737727	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2140418	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2273006	0.94[ASW][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs2293242	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2473613	0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap]
rs2473615	0.89[GIH][hapmap]
rs2504162	0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap]
rs2504168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2985	0.94[ASW][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs3734262	0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs3800451	0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap]
rs4432973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646933	0.86[YRI][hapmap]
rs4646949	0.88[GIH][hapmap]
rs6457797	0.88[LWK][hapmap];0.86[YRI][hapmap]
rs6457799	0.82[MEX][hapmap]
rs6905468	0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs6907619	0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs6918872	0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap]
rs6932857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6941065	0.86[LWK][hapmap];0.84[MKK][hapmap]
rs7739385	0.86[YRI][hapmap]
rs7753949	0.91[GIH][hapmap]
rs7759369	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820078	0.81[JPT][hapmap]
rs820079	0.81[JPT][hapmap]
rs820084	0.81[JPT][hapmap]
rs820097	0.81[JPT][hapmap]
rs847845	0.82[MEX][hapmap]
rs847846	0.95[GIH][hapmap]
rs847847	0.80[ASN][1000 genomes]
rs847848	0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.80[ASN][1000 genomes]
rs847850	0.85[CEU][hapmap]
rs847851	0.84[GIH][hapmap]
rs9296139	0.88[ASW][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];0.96[YRI][hapmap]
rs9357188	0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap]
rs9368834	0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs9380469	0.82[CEU][hapmap]
rs9380482	0.81[ASN][1000 genomes]
rs9784818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv885797	chr6:34791027-34980601	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2177381	PRDM7	trans	multi-tissue	Pritchard
rs2177381	TAF11	cis	lymphoblastoid	seeQTL
rs2177381	C6orf107	Cis_1M	lymphoblastoid	RTeQTL
rs2177381	UHRF1BP1	cis	parietal	SCAN
rs2177381	TAF11	cis	cerebellum	SCAN
rs2177381	TAF11	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34925600-34984800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:34926800-34992200	Weak transcription	Small Intestine	intestine
3	chr6:34932400-34981800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr6:34939400-34978200	Weak transcription	Psoas Muscle	Psoas
5	chr6:34939400-35016000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:34959200-34979000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:34960200-34979200	Weak transcription	HUVEC	blood vessel
8	chr6:34960200-34988200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:34961000-34985200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:34961200-34983400	Weak transcription	Fetal Kidney	kidney
11	chr6:34961600-34982200	Weak transcription	Right Ventricle	heart
12	chr6:34962200-34982200	Weak transcription	Hela-S3	cervix
13	chr6:34962200-34984800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:34962800-34978800	Weak transcription	Fetal Lung	lung
15	chr6:34962800-34983600	Weak transcription	Osteobl	bone
16	chr6:34962800-34985200	Weak transcription	Brain Germinal Matrix	brain
17	chr6:34963000-34978000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr6:34963000-34979400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:34963000-34982200	Weak transcription	Aorta	Aorta
20	chr6:34963000-34982200	Weak transcription	Pancreas	Pancrea
21	chr6:34963000-34982400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:34963000-34982400	Weak transcription	Fetal Stomach	stomach
23	chr6:34963000-34982600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr6:34963000-34985000	Weak transcription	Fetal Brain Female	brain
25	chr6:34963000-34985200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr6:34963000-34985400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr6:34963000-34985600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr6:34963000-34985600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr6:34963000-34985600	Weak transcription	NHEK	skin
30	chr6:34963000-34987800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:34963000-34989400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr6:34963200-34982200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:34963600-34978600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:34963600-34978800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr6:34963600-34978800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr6:34963600-34981600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:34963600-34982000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:34963600-34982000	Weak transcription	Adipose Nuclei	Adipose
39	chr6:34963600-34983400	Weak transcription	Colonic Mucosa	Colon
40	chr6:34963600-34990000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:34963600-35006600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr6:34964200-34985400	Weak transcription	Primary B cells from peripheral blood	blood
43	chr6:34965800-34985400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:34965800-34985400	Weak transcription	HepG2	liver
45	chr6:34966000-34978600	Weak transcription	HSMM	muscle
46	chr6:34966000-34982200	Weak transcription	Left Ventricle	heart
47	chr6:34966000-34985400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr6:34966200-34982400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr6:34966400-34985000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:34967000-34980600	Weak transcription	Lung	lung

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