Variant report

Variant	rs2278536
Chromosome Location	chr2:86258784-86258785
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:86258463-86258850	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86253744..86255474-chr2:86257565..86259502,2	MCF-7	breast:

Variant related genes	Relation type
POLR1A	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10175330	1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[TSI][hapmap]
rs10178120	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10178540	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10184462	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10185452	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10187150	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs10496318	1.00[CHB][hapmap]
rs1057893	1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[TSI][hapmap]
rs11395	1.00[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap]
rs11885380	1.00[CHB][hapmap]
rs11899254	1.00[CHB][hapmap]
rs12328100	1.00[ASW][hapmap]
rs12469762	0.82[ASW][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap]
rs12475079	1.00[CHB][hapmap]
rs12475126	1.00[CHB][hapmap]
rs12477274	1.00[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap]
rs12478097	1.00[CHB][hapmap]
rs12714162	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12714166	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12714171	1.00[CHB][hapmap]
rs12714172	1.00[CHB][hapmap]
rs12714175	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12714177	0.82[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap]
rs12994838	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12996308	1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[TSI][hapmap]
rs12997506	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13000793	0.81[CHD][hapmap]
rs13001470	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13004643	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13024123	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13027248	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13028023	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs13403186	0.89[CEU][hapmap]
rs1424522	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs1540391	0.82[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap]
rs17027013	1.00[CHB][hapmap]
rs2241438	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs2278083	1.00[CHB][hapmap]
rs2288113	1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[TSI][hapmap]
rs2288115	1.00[CHB][hapmap]
rs2289239	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2367203	1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[TSI][hapmap]
rs2367204	1.00[CHB][hapmap]
rs34478066	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34723687	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770059	0.92[JPT][hapmap]
rs3770062	1.00[CHB][hapmap]
rs3770065	1.00[CHB][hapmap]
rs3770067	1.00[CHB][hapmap]
rs3770075	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3821017	0.85[CEU][hapmap]
rs4374375	1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[TSI][hapmap]
rs4402761	1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[TSI][hapmap]
rs4422155	1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[TSI][hapmap]
rs4450596	1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[TSI][hapmap]
rs4544439	1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[TSI][hapmap]
rs4597526	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4832019	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4832234	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4832236	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6547661	1.00[CHB][hapmap]
rs6547665	0.82[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap]
rs6707029	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs6725372	1.00[CHB][hapmap]
rs6729732	1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[TSI][hapmap]
rs6731995	1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[TSI][hapmap]
rs6735014	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6737950	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs6740044	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6749090	0.89[CEU][hapmap];0.80[TSI][hapmap]
rs6757387	1.00[CHB][hapmap]
rs715334	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap]
rs735738	1.00[CHB][hapmap]
rs7422930	0.84[TSI][hapmap]
rs7560376	1.00[JPT][hapmap]
rs7563742	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7566721	1.00[CHB][hapmap]
rs7572386	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7590445	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7609008	1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[TSI][hapmap]
rs8244	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs876242	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[TSI][hapmap]
rs9309632	1.00[CHB][hapmap]
rs9309633	1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap]
rs9653508	0.89[CEU][hapmap]
rs9653569	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001104	chr2:86182021-86271923	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv535807	chr2:86182021-86271923	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	esv32617	chr2:86256641-86260285	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs2278536	IMMT	Cis_1M	lymphoblastoid	RTeQTL
rs2278536	REEP1	cis	parietal	SCAN
rs2278536	IMMT	cis	Artery Aorta	GTEx
rs2278536	ST3GAL5	cis	cerebellum	SCAN
rs2278536	IMMT	cis	lymphoblastoid	seeQTL
rs2278536	IMMT	cis	multi-tissue	Pritchard
rs2278536	POLR1A	cis	lymphoblastoid	seeQTL
rs2278536	IMMT	cis	cerebellum	SCAN
rs2278536	MRPL35	cis	cerebellum	SCAN
rs2278536	MRPL35	cis	parietal	SCAN
rs2278536	IMMT	cis	Whole Blood	GTEx
rs2278536	MRPL35	cis	lymphoblastoid	seeQTL
rs2278536	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs2278536	IMMT	cis	Esophagus Muscularis	GTEx
rs2278536	LOC90784	Cis_1M	lymphoblastoid	RTeQTL
rs2278536	IMMT	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86245400-86263400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:86250800-86262200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:86251000-86261000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr2:86251000-86262000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:86251000-86262600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:86251000-86262800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:86251200-86261600	Strong transcription	NH-A	brain
8	chr2:86251200-86261800	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:86251200-86262400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:86251200-86262800	Strong transcription	Fetal Brain Female	brain
11	chr2:86251200-86263200	Strong transcription	A549	lung
12	chr2:86251200-86273200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:86251200-86281400	Strong transcription	H9 Cell Line	embryonic stem cell
14	chr2:86251200-86283000	Strong transcription	HepG2	liver
15	chr2:86251200-86283200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:86251200-86285000	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr2:86251200-86285200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:86251400-86261000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:86251400-86261000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:86251400-86261200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:86251400-86262000	Strong transcription	Osteobl	bone
22	chr2:86251400-86262800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:86251400-86263400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:86251600-86261600	Strong transcription	HMEC	breast
25	chr2:86251800-86259400	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr2:86251800-86262000	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:86251800-86262400	Strong transcription	Fetal Intestine Small	intestine
28	chr2:86252000-86262000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:86252000-86331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:86252200-86262000	Strong transcription	GM12878-XiMat	blood
31	chr2:86252200-86262400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:86252200-86262600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:86252200-86282600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:86252200-86285200	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr2:86252400-86258800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr2:86252400-86261000	Strong transcription	Dnd41	blood
37	chr2:86252400-86261600	Strong transcription	Esophagus	oesophagus
38	chr2:86252400-86262200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:86252400-86262400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:86252400-86262400	Strong transcription	NHEK	skin
41	chr2:86252400-86262600	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr2:86252400-86263000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:86252400-86283200	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr2:86252600-86259000	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr2:86252600-86259400	Strong transcription	Primary B cells from cord blood	blood
46	chr2:86252600-86260200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:86252600-86260800	Strong transcription	Ovary	ovary
48	chr2:86252600-86261000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr2:86252600-86261600	Strong transcription	Pancreas	Pancrea
50	chr2:86252600-86262600	Strong transcription	Hela-S3	cervix

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