Variant report

Variant	rs11600668
Chromosome Location	chr11:47193566-47193567
allele	A/G
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	chr11:47192905-47194068	K562	blood:	n/a	n/a
2	POLR2A	chr11:47192694-47195552	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr11:47193510-47193762	GM12878	blood:	n/a	n/a
4	POLR2A	chr11:47192839-47193683	K562	blood:	n/a	n/a
5	POLR2A	chr11:47192191-47195978	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr11:47193284-47193573	K562	blood:	n/a	n/a
7	POLR2A	chr11:47193273-47194344	GM12878	blood:	n/a	n/a
8	POLR2A	chr11:47192556-47193650	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr11:47193553-47193688	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ARFGAP2	TF binding region
ENSG00000270060	TF binding region

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10466478	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10501319	0.83[CHB][hapmap];0.89[GIH][hapmap]
rs1055447	0.83[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs1060573	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10769227	0.83[CHB][hapmap]
rs10769230	0.82[ASN][1000 genomes]
rs10769233	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10769234	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10769239	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10838644	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs10838646	0.83[CHB][hapmap]
rs10838652	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs10838654	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10838658	0.82[CHB][hapmap]
rs10838659	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10838660	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10838662	0.83[CHB][hapmap];0.89[GIH][hapmap]
rs10838663	0.83[CHB][hapmap]
rs10838664	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs10838681	0.83[CHD][hapmap]
rs11039074	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039086	0.92[ASN][1000 genomes]
rs11039097	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11039105	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11039107	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11039112	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11039119	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039124	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039134	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11601798	0.85[CHB][hapmap]
rs12224096	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12291341	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12417519	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs12574410	0.86[CHB][hapmap]
rs12796744	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12807887	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1872896	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1965952	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1976142	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1976143	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2018527	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2029298	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2087215	0.83[CHB][hapmap];0.89[GIH][hapmap]
rs2279438	0.83[CHB][hapmap]
rs2279439	0.83[CHB][hapmap];0.80[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap]
rs4237547	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4319472	0.95[CEU][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4528282	0.82[CHB][hapmap]
rs4548577	0.83[CHB][hapmap]
rs4567413	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4579897	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4587689	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs4752951	0.82[CHB][hapmap]
rs4752952	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4752957	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4752962	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4752963	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4752965	0.83[CHB][hapmap]
rs4752967	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4752969	0.83[CHB][hapmap];0.89[GIH][hapmap]
rs4752971	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57323109	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6485721	0.85[ASN][1000 genomes]
rs6485722	0.84[ASN][1000 genomes]
rs6485726	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs6485739	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7103581	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7108902	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7111270	0.83[CHB][hapmap]
rs7111764	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7112854	0.82[CHB][hapmap];0.86[GIH][hapmap]
rs7118546	0.84[EUR][1000 genomes]
rs7119952	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7121418	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7124648	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7125807	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.85[ASN][1000 genomes]
rs7126005	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7128325	0.85[ASN][1000 genomes]
rs7128650	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7130006	0.83[CHB][hapmap];0.92[GIH][hapmap]
rs7130947	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs747650	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7479189	0.95[CEU][hapmap];0.89[ASN][1000 genomes]
rs7931260	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs7935346	0.86[GIH][hapmap]
rs7937101	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7937410	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs7937950	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7940240	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs7942473	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7945315	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7946709	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7947878	0.81[ASN][1000 genomes]
rs7950753	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs923324	0.82[CHB][hapmap]
rs9633886	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[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	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv897324	chr11:47193566-47212032	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11600668	F2	cis	cerebellum	SCAN
rs11600668	C11orf49	cis	parietal	SCAN
rs11600668	DDB2	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47175400-47197600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47176000-47196600	Strong transcription	Fetal Intestine Small	intestine
3	chr11:47176800-47196600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:47178000-47197000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr11:47178200-47194000	Strong transcription	Dnd41	blood
6	chr11:47178800-47196800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:47180600-47196600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr11:47181400-47197000	Weak transcription	Right Atrium	heart
9	chr11:47182000-47196400	Strong transcription	Hela-S3	cervix
10	chr11:47182200-47194800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr11:47182200-47197000	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr11:47182400-47196400	Strong transcription	Fetal Intestine Large	intestine
13	chr11:47183200-47194000	Strong transcription	Primary B cells from peripheral blood	blood
14	chr11:47183200-47197000	Strong transcription	Placenta	Placenta
15	chr11:47183200-47197200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr11:47183400-47193800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr11:47183400-47194600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:47183400-47194600	Strong transcription	Colonic Mucosa	Colon
19	chr11:47183400-47196600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr11:47183400-47197000	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr11:47183400-47197000	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr11:47183400-47197000	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr11:47183600-47193800	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr11:47183600-47194200	Strong transcription	Fetal Thymus	thymus
25	chr11:47183600-47196400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:47183600-47196600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr11:47183600-47197000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr11:47183600-47197000	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr11:47183800-47196800	Strong transcription	NHLF	lung
30	chr11:47184000-47193600	Strong transcription	Adipose Nuclei	Adipose
31	chr11:47184000-47194000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr11:47184000-47196800	Strong transcription	Duodenum Mucosa	Duodenum
33	chr11:47184200-47196000	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr11:47184400-47193800	Strong transcription	Pancreas	Pancrea
35	chr11:47184400-47194000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr11:47184400-47194400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr11:47184400-47196400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr11:47184400-47197000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr11:47184600-47194000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr11:47184600-47196400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr11:47184600-47196600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr11:47184800-47195200	Strong transcription	Primary B cells from cord blood	blood
43	chr11:47184800-47196600	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr11:47184800-47197000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr11:47185000-47195600	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr11:47185200-47193800	Strong transcription	Brain Germinal Matrix	brain
47	chr11:47185200-47195600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr11:47185200-47196600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr11:47185400-47193800	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr11:47185400-47195600	Strong transcription	Muscle Satellite Cultured Cells	--

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