Variant report

Variant	rs11868785
Chromosome Location	chr17:34139218-34139219
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:34135622-34141134	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr17:34138783-34139267	GM12891	blood:	n/a	n/a
3	POLR2A	chr17:34138752-34139631	GM12892	blood:	n/a	n/a
4	POLR2A	chr17:34138414-34139641	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr17:34138844-34139460	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr17:34138821-34139493	K562	blood:	n/a	n/a
7	POLR2A	chr17:34138696-34139549	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr17:34138722-34139493	GM12878	blood:	n/a	n/a
9	POLR2A	chr17:34138979-34139550	GM12891	blood:	n/a	n/a
10	POLR2A	chr17:34135340-34139464	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr17:34138814-34139519	GM12891	blood:	n/a	n/a
12	USF2	chr17:34138898-34139332	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr17:34138724-34139560	GM12892	blood:	n/a	n/a
14	POLR2A	chr17:34138972-34139505	HepG2	liver:	n/a	n/a
15	POLR2A	chr17:34138939-34139273	GM12878	blood:	n/a	n/a
16	POLR2A	chr17:34138755-34139543	SK-N-MC	brain:	n/a	n/a
17	POLR2A	chr17:34135774-34139332	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr17:34138817-34139396	GM12892	blood:	n/a	n/a
19	POLR2A	chr17:34138771-34139479	GM12892	blood:	n/a	n/a
20	POLR2A	chr17:34138708-34139347	K562	blood:	n/a	n/a
21	POLR2A	chr17:34138844-34139417	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr17:34138691-34139342	GM12878	blood:	n/a	n/a
23	POLR2A	chr17:34138897-34139306	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:27619493..27621031-chr17:34136580..34139229,2	MCF-7	breast:
2	chr17:34137709..34141485-chr17:34149369..34151902,3	MCF-7	breast:
3	chr17:34089535..34095936-chr17:34135210..34140609,14	MCF-7	breast:
4	chr17:34138831..34141279-chr17:34143427..34145542,2	MCF-7	breast:
5	chr17:34138348..34140751-chr17:34159365..34161956,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000267578	TF binding region
ENSG00000172660	Chromatin interaction
ENSG00000267347	Chromatin interaction
ENSG00000129270	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs11650409	0.89[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs11650668	0.83[AMR][1000 genomes]
rs11652192	0.87[EUR][1000 genomes]
rs11652536	0.88[CEU][hapmap]
rs11653051	0.89[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs11653282	0.85[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs11655533	0.89[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs11657908	0.89[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs11658222	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2014839	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2107538	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs2280789	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2291299	0.80[CEU][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs2306630	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28595279	0.83[AMR][1000 genomes]
rs35517765	0.83[ASN][1000 genomes]
rs3760326	0.82[EUR][1000 genomes]
rs3785764	1.00[CEU][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs3809769	0.88[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs3817655	1.00[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap]
rs4079183	0.83[AMR][1000 genomes]
rs4251702	0.88[CEU][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs4251703	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4251719	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4251724	0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4251727	0.86[EUR][1000 genomes]
rs4251729	0.90[EUR][1000 genomes]
rs4251737	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4251749	0.83[AMR][1000 genomes]
rs4251751	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs4251752	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs4251769	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4251788	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4325615	0.83[AMR][1000 genomes]
rs4795089	0.88[CEU][hapmap];0.95[TSI][hapmap]
rs4795090	0.81[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4795091	0.90[EUR][1000 genomes]
rs4795092	0.90[EUR][1000 genomes]
rs4795093	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4795095	0.88[CEU][hapmap];0.88[YRI][hapmap]
rs4795096	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs4796107	0.88[CEU][hapmap];0.95[TSI][hapmap]
rs4796108	0.86[CEU][hapmap]
rs4796109	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4796112	0.83[ASW][hapmap];0.88[CEU][hapmap];0.89[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4796113	0.87[EUR][1000 genomes]
rs4796114	0.85[EUR][1000 genomes]
rs4796115	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs4796118	0.89[GIH][hapmap];0.80[LWK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4796119	0.87[CEU][hapmap];0.95[TSI][hapmap]
rs4796120	0.88[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap]
rs4796123	1.00[CEU][hapmap];0.84[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs4796128	0.80[CEU][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs55950249	0.83[EUR][1000 genomes]
rs6505496	0.80[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6505498	0.85[ASN][1000 genomes]
rs8080959	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9303691	0.83[ASW][hapmap];0.88[CEU][hapmap];0.89[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs9303692	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9889274	0.90[TSI][hapmap]
rs9889874	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9894083	0.84[EUR][1000 genomes]
rs9898132	0.88[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap]
rs9898152	0.83[ASW][hapmap];0.88[CEU][hapmap];0.89[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap]
rs9899866	0.89[GIH][hapmap];0.90[TSI][hapmap]
rs9900236	0.89[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs9900473	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9900563	0.80[EUR][1000 genomes]
rs9904675	0.89[GIH][hapmap];0.90[TSI][hapmap]
rs9907121	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9907295	0.89[GIH][hapmap];0.90[TSI][hapmap]
rs9907588	0.85[EUR][1000 genomes]
rs9908011	0.89[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs9909050	0.88[CEU][hapmap];0.89[GIH][hapmap];0.86[TSI][hapmap]
rs9909416	0.85[CEU][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9911598	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9913488	0.89[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs9914401	0.83[ASW][hapmap];0.88[CEU][hapmap];0.89[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11868785	RDM1	cis	multi-tissue	Pritchard
rs11868785	RAD52B	cis	multi-tissue	Pritchard
rs11868785	RDM1	cis	lymphoblastoid	seeQTL
rs11868785	CCL5	cis	lymphoblastoid	seeQTL
rs11868785	RDM1	cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:34137000-34139400	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr17:34137200-34139400	Transcr. at gene 5' and 3'	K562	blood
3	chr17:34137600-34141200	Weak transcription	Aorta	Aorta
4	chr17:34137600-34143400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr17:34137600-34149200	Weak transcription	Gastric	stomach
6	chr17:34137800-34139400	Enhancers	Primary B cells from peripheral blood	blood
7	chr17:34137800-34139400	Enhancers	Liver	Liver
8	chr17:34137800-34139800	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr17:34137800-34142800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr17:34137800-34142800	Weak transcription	Placenta	Placenta
11	chr17:34137800-34143600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr17:34137800-34143800	Weak transcription	Left Ventricle	heart
13	chr17:34137800-34144800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr17:34137800-34145000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr17:34137800-34149200	Weak transcription	Esophagus	oesophagus
16	chr17:34137800-34149800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr17:34137800-34152000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr17:34137800-34154000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr17:34138000-34139400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
20	chr17:34138000-34139400	Enhancers	Brain Hippocampus Middle	brain
21	chr17:34138000-34139600	Enhancers	Brain Cingulate Gyrus	brain
22	chr17:34138000-34140000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr17:34138000-34140200	Weak transcription	Stomach Mucosa	stomach
24	chr17:34138000-34140600	Weak transcription	Fetal Intestine Small	intestine
25	chr17:34138000-34141600	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr17:34138000-34143000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr17:34138000-34143000	Weak transcription	Fetal Muscle Leg	muscle
28	chr17:34138000-34144800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr17:34138000-34144800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr17:34138000-34145200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr17:34138000-34146200	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr17:34138000-34146800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr17:34138000-34149600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr17:34138000-34153400	Weak transcription	Right Ventricle	heart
35	chr17:34138000-34164200	Weak transcription	Colonic Mucosa	Colon
36	chr17:34138200-34139400	Enhancers	Colon Smooth Muscle	Colon
37	chr17:34138200-34139400	Enhancers	Fetal Lung	lung
38	chr17:34138200-34139400	Enhancers	Stomach Smooth Muscle	stomach
39	chr17:34138200-34139600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr17:34138200-34139800	Weak transcription	Right Atrium	heart
41	chr17:34138200-34140000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr17:34138200-34140000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr17:34138200-34140600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr17:34138200-34141200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr17:34138200-34142800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr17:34138200-34143000	Weak transcription	Psoas Muscle	Psoas
47	chr17:34138200-34145800	Weak transcription	NHDF-Ad	bronchial
48	chr17:34138200-34149400	Weak transcription	HSMMtube	muscle
49	chr17:34138200-34149600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr17:34138200-34151600	Weak transcription	Fetal Heart	heart

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