Variant report

Variant	rs10153801
Chromosome Location	chr2:113294298-113294299
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113292898..113296268-chr2:113298065..113301021,4	K562	blood:
2	chr2:113294231..113297135-chr2:113298138..113301190,3	MCF-7	breast:
3	chr2:113294101..113296861-chr2:113298978..113301563,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125630	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10153558	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10864905	0.85[CHB][hapmap]
rs11123137	0.91[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs11123139	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11644	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs11675730	0.82[ASN][1000 genomes]
rs11676962	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11677050	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs11899598	0.96[CEU][hapmap];0.83[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs12465446	0.88[EUR][1000 genomes]
rs13015669	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13030618	0.96[CEU][hapmap];0.83[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1437673	0.96[CEU][hapmap];0.95[CHB][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1437675	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1545133	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1595388	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17043158	0.96[CEU][hapmap];0.83[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17043167	0.96[CEU][hapmap];0.82[CHB][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2304555	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs28542310	0.86[EUR][1000 genomes]
rs34082454	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35419160	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3816140	0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs3816141	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs3849314	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3910512	0.87[EUR][1000 genomes]
rs3961775	0.82[ASN][1000 genomes]
rs3980067	0.94[ASN][1000 genomes]
rs41278940	0.83[ASN][1000 genomes]
rs4443006	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4849072	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4849073	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4849074	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4849076	0.83[ASN][1000 genomes]
rs56010201	0.87[EUR][1000 genomes]
rs60703755	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62157527	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6542059	0.83[EUR][1000 genomes]
rs6542060	0.82[EUR][1000 genomes]
rs6542061	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6717635	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs6718241	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6718489	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs6760014	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7568539	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7569407	0.92[CEU][hapmap];0.83[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs7578724	0.86[CHB][hapmap]
rs7580213	0.85[EUR][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	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10153801	POLR1B	cis	parietal	SCAN
rs10153801	POLR1B	cis	cerebellum	SCAN
rs10153801	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs10153801	RGPD8	cis	Artery Tibial	GTEx
rs10153801	FBLN7	cis	parietal	SCAN
rs10153801	RGPD8	cis	Nerve Tibial	GTEx
rs10153801	RGPD8	cis	Muscle Skeletal	GTEx
rs10153801	TTL	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113260800-113298800	Weak transcription	Fetal Heart	heart
2	chr2:113270600-113298800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr2:113279000-113299200	Weak transcription	Psoas Muscle	Psoas
4	chr2:113281200-113299000	Weak transcription	Colonic Mucosa	Colon
5	chr2:113287000-113298800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:113287000-113298800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:113287000-113299000	Weak transcription	Fetal Intestine Small	intestine
8	chr2:113287000-113299000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:113287200-113298800	Weak transcription	Fetal Brain Male	brain
10	chr2:113287200-113298800	Weak transcription	Pancreas	Pancrea
11	chr2:113287200-113299000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:113287400-113298800	Weak transcription	Hela-S3	cervix
13	chr2:113287600-113298600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:113287600-113299000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:113287800-113298800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr2:113287800-113298800	Weak transcription	Fetal Intestine Large	intestine
17	chr2:113287800-113299000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr2:113287800-113299000	Weak transcription	Liver	Liver
19	chr2:113287800-113299400	Weak transcription	Spleen	Spleen
20	chr2:113288000-113298600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:113288000-113299000	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:113288200-113298400	Weak transcription	GM12878-XiMat	blood
23	chr2:113288200-113298600	Weak transcription	Brain Substantia Nigra	brain
24	chr2:113288200-113298800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:113288200-113299000	Weak transcription	Right Ventricle	heart
26	chr2:113288200-113299000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:113288400-113299000	Weak transcription	Placenta	Placenta
28	chr2:113288800-113298200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr2:113288800-113299000	Weak transcription	Fetal Lung	lung
30	chr2:113288800-113299200	Weak transcription	Esophagus	oesophagus
31	chr2:113288800-113299200	Weak transcription	Gastric	stomach
32	chr2:113289000-113299000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:113289200-113299000	Weak transcription	Fetal Kidney	kidney
34	chr2:113289400-113298600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr2:113289400-113299000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr2:113289600-113298800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr2:113289600-113299000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:113289800-113298600	Weak transcription	K562	blood
39	chr2:113289800-113298800	Weak transcription	Aorta	Aorta
40	chr2:113289800-113299000	Weak transcription	NHDF-Ad	bronchial
41	chr2:113289800-113299200	Weak transcription	Ovary	ovary
42	chr2:113290000-113298400	Weak transcription	Primary B cells from cord blood	blood
43	chr2:113290000-113298800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:113290000-113298800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:113290000-113298800	Weak transcription	NH-A	brain
46	chr2:113290000-113299000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr2:113290000-113299000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr2:113290200-113298600	Weak transcription	Primary T cells from cord blood	blood
49	chr2:113290200-113298800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr2:113290200-113298800	Weak transcription	Primary monocytes fromperipheralblood	blood

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