Variant report

Variant	rs2247472
Chromosome Location	chr1:160976238-160976239
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160976230..160985885-chr1:160986202..160992598,31	K562	blood:
2	chr1:160972146..160973974-chr1:160974703..160977158,2	K562	blood:
3	chr1:160962192..160965720-chr1:160976093..160980486,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158769	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10737178	0.83[CHB][hapmap];0.87[CHD][hapmap]
rs10908820	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12132502	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12758348	0.86[ASN][1000 genomes]
rs2039223	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2184065	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2246145	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2246485	0.91[CEU][hapmap]
rs2249933	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2250174	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2250193	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2250304	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2256625	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs2481076	0.96[ASN][1000 genomes]
rs2481077	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2483139	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs2483141	0.92[CEU][hapmap];0.92[CHB][hapmap]
rs2483142	0.80[EUR][1000 genomes]
rs2990706	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3007155	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4396136	0.81[MEX][hapmap]
rs4483427	0.81[ASN][1000 genomes]
rs6427571	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6677526	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7512280	0.82[ASN][1000 genomes]
rs7542911	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs790055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs790056	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv548058	chr1:160925455-160989614	Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2247472	OR10R2	cis	parietal	SCAN
rs2247472	TSTD1	cis	Artery Tibial	GTEx
rs2247472	F11R	cis	parietal	SCAN
rs2247472	F11R	Cis_1M	lymphoblastoid	RTeQTL
rs2247472	PAQR6	cis	cerebellum	SCAN
rs2247472	TSTD1	cis	Adipose Subcutaneous	GTEx
rs2247472	F11R	cis	lymphoblastoid	seeQTL
rs2247472	OR6K3	cis	cerebellum	SCAN
rs2247472	TSTD1	cis	Nerve Tibial	GTEx
rs2247472	NHLH1	cis	parietal	SCAN
rs2247472	RXFP4	cis	parietal	SCAN
rs2247472	F11R	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160960400-160978400	Weak transcription	Fetal Lung	lung
2	chr1:160960600-160977400	Weak transcription	Fetal Kidney	kidney
3	chr1:160960600-160981600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:160963400-160983000	Weak transcription	HSMMtube	muscle
5	chr1:160967800-160978200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:160967800-160978800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:160968000-160976800	Weak transcription	Brain Angular Gyrus	brain
8	chr1:160969800-160978400	Weak transcription	A549	lung
9	chr1:160970000-160982800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:160970600-160981800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:160970600-160981800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:160970600-160982400	Weak transcription	Dnd41	blood
13	chr1:160970600-160982600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:160970600-160983000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:160970600-160983000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:160970600-160983000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:160970800-160981600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:160970800-160982600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:160970800-160983000	Weak transcription	HSMM	muscle
20	chr1:160971000-160977400	Weak transcription	HUVEC	blood vessel
21	chr1:160971000-160977800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:160971000-160979400	Weak transcription	Ovary	ovary
23	chr1:160971000-160981400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr1:160971000-160981400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:160971000-160981600	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr1:160971000-160982000	Weak transcription	GM12878-XiMat	blood
27	chr1:160971000-160982600	Weak transcription	Thymus	Thymus
28	chr1:160971000-160983200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr1:160971200-160976400	Weak transcription	Gastric	stomach
30	chr1:160971200-160976400	Weak transcription	Pancreas	Pancrea
31	chr1:160971200-160981200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr1:160971200-160981800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:160971200-160981800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr1:160971200-160981800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:160971200-160981800	Weak transcription	Fetal Thymus	thymus
36	chr1:160971200-160982800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:160971200-160983000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:160971200-160983000	Weak transcription	Colonic Mucosa	Colon
39	chr1:160971400-160978400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:160971400-160978800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:160971400-160981200	Weak transcription	Primary B cells from cord blood	blood
42	chr1:160971400-160981400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr1:160971400-160981800	Weak transcription	Small Intestine	intestine
44	chr1:160971400-160983000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:160971600-160978400	Weak transcription	Esophagus	oesophagus
46	chr1:160971600-160978600	Weak transcription	Fetal Intestine Large	intestine
47	chr1:160971600-160981000	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr1:160971600-160981600	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:160971600-160982600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr1:160971600-160983000	Weak transcription	Left Ventricle	heart

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