Variant report

Variant	rs2271192
Chromosome Location	chr12:56531154-56531155
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56530736-56531756	K562	blood:	n/a	n/a
2	POLR2A	chr12:56530887-56531314	HL-60	blood:	n/a	n/a
3	POLR2A	chr12:56531009-56531157	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr12:56530951-56531244	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr12:56530205-56531266	K562	blood:	n/a	n/a
6	POLR2A	chr12:56529927-56532864	K562	blood:	n/a	n/a
7	POLR2A	chr12:56530005-56532515	K562	blood:	n/a	n/a
8	POLR2A	chr12:56530854-56531159	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56518356..56534331-chr12:56534720..56548698,49	MCF-7	breast:
2	chr12:56530580..56533098-chr12:56544612..56547125,6	MCF-7	breast:
3	chr12:56529351..56534783-chr12:56551483..56555184,6	MCF-7	breast:

No data

Variant related genes	Relation type
ESYT1	TF binding region
ENSG00000196465	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000092841	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10747761	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs10747763	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11171745	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.80[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11171752	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171772	1.00[JPT][hapmap]
rs11171777	1.00[JPT][hapmap]
rs11834728	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12229022	0.84[ASN][1000 genomes]
rs12320265	1.00[JPT][hapmap]
rs1274298	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs1274494	1.00[CHD][hapmap]
rs1274502	1.00[JPT][hapmap]
rs12810816	0.92[CEU][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap]
rs1405859	1.00[JPT][hapmap]
rs1689512	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.80[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17118313	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17118317	0.85[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs17118333	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2271188	0.94[ASN][1000 genomes]
rs2271190	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2456972	1.00[CHD][hapmap]
rs2463365	1.00[JPT][hapmap]
rs2629453	1.00[JPT][hapmap]
rs2640569	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.80[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2695783	1.00[JPT][hapmap]
rs2695784	1.00[JPT][hapmap]
rs28676339	0.94[ASN][1000 genomes]
rs2930788	1.00[JPT][hapmap]
rs2950573	1.00[JPT][hapmap]
rs35436573	0.84[TSI][hapmap]
rs35509412	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3759096	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3802996	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3809130	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4759218	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs55887836	0.87[ASN][1000 genomes]
rs56851901	0.94[ASN][1000 genomes]
rs57280585	0.94[ASN][1000 genomes]
rs58476735	0.94[ASN][1000 genomes]
rs58548156	0.94[ASN][1000 genomes]
rs58663297	0.94[ASN][1000 genomes]
rs60396934	0.94[ASN][1000 genomes]
rs6581091	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs703823	1.00[JPT][hapmap]
rs7311008	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[ASN][1000 genomes]
rs73340323	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7489249	1.00[JPT][hapmap]
rs772922	1.00[CHD][hapmap]
rs773120	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs773121	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs773122	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs773123	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs773643	1.00[GIH][hapmap]
rs773649	1.00[CEU][hapmap];0.92[GIH][hapmap];0.89[TSI][hapmap]
rs773658	1.00[JPT][hapmap]
rs773659	1.00[JPT][hapmap]
rs7962107	1.00[JPT][hapmap]
rs812826	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.92[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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs2271192	RPL41	cis	parietal	SCAN
rs2271192	ESYT1	cis	cerebellum	SCAN
rs2271192	RPS26P10	trans	multi-tissue	Pritchard
rs2271192	OR6C1	cis	cerebellum	SCAN
rs2271192	KIF5A	cis	parietal	SCAN
rs2271192	CCDC4	trans	multi-tissue	Pritchard
rs2271192	LOC441377	trans	multi-tissue	Pritchard
rs2271192	ERBB3	cis	parietal	SCAN
rs2271192	LOC644934	trans	multi-tissue	Pritchard
rs2271192	LOC441502	trans	multi-tissue	Pritchard
rs2271192	SUOX	cis	cerebellum	SCAN
rs2271192	MADCAM1	trans	multi-tissue	Pritchard
rs2271192	HOXC8	cis	cerebellum	SCAN
rs2271192	RPS26	cis	lymphoblastoid	seeQTL
rs2271192	RPS26	cis	multi-tissue	Pritchard
rs2271192	SP1	cis	parietal	SCAN
rs2271192	KRT4	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56523200-56533400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:56523600-56537200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:56523800-56537000	Weak transcription	Right Atrium	heart
4	chr12:56523800-56539400	Strong transcription	NHEK	skin
5	chr12:56524000-56537000	Strong transcription	Fetal Intestine Small	intestine
6	chr12:56524200-56539200	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr12:56524200-56539200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:56524200-56539400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:56524200-56539400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:56524200-56539400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:56524200-56539400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:56524200-56539400	Strong transcription	NH-A	brain
13	chr12:56524400-56535000	Genic enhancers	Primary T cells fromperipheralblood	blood
14	chr12:56524400-56535200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr12:56524400-56535200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr12:56524400-56535400	Strong transcription	Spleen	Spleen
17	chr12:56524400-56536600	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr12:56524400-56536800	Strong transcription	HMEC	breast
19	chr12:56524400-56537000	Strong transcription	Fetal Intestine Large	intestine
20	chr12:56524400-56539000	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr12:56524400-56539000	Strong transcription	Rectal Smooth Muscle	rectum
22	chr12:56524400-56539000	Strong transcription	HSMMtube	muscle
23	chr12:56524400-56539200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr12:56524400-56539200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:56524400-56539200	Strong transcription	Fetal Stomach	stomach
26	chr12:56524400-56539400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:56524400-56539400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:56524400-56539400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:56524400-56539400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:56524400-56539400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:56524400-56539400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:56524400-56539400	Strong transcription	Liver	Liver
33	chr12:56524400-56539600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:56524600-56536000	Strong transcription	Adipose Nuclei	Adipose
35	chr12:56524600-56536000	Strong transcription	Lung	lung
36	chr12:56524600-56536600	Strong transcription	Stomach Smooth Muscle	stomach
37	chr12:56524600-56537400	Strong transcription	Fetal Muscle Leg	muscle
38	chr12:56524600-56537600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
39	chr12:56524600-56538000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:56524600-56538600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:56524600-56538800	Strong transcription	Fetal Brain Female	brain
42	chr12:56524600-56539000	Strong transcription	Colon Smooth Muscle	Colon
43	chr12:56524600-56539200	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr12:56524600-56539400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:56524600-56539400	Strong transcription	HSMM	muscle
46	chr12:56524600-56539400	Strong transcription	NHDF-Ad	bronchial
47	chr12:56524800-56531800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:56524800-56536800	Strong transcription	Fetal Muscle Trunk	muscle
49	chr12:56525000-56531800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:56525000-56531800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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