Variant report

Variant	rs4795089
Chromosome Location	chr17:34119397-34119398
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:34118856..34121168-chr17:34121467..34123390,2	MCF-7	breast:
2	chr17:34119059..34120635-chr17:34120738..34123600,2	K562	blood:

Variant related genes	Relation type
ENSG00000129270	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs11650409	0.87[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap]
rs11652192	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11652536	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs11653051	0.87[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap]
rs11653204	0.81[ASN][1000 genomes]
rs11653282	0.87[CEU][hapmap];0.95[TSI][hapmap]
rs11655533	0.87[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap]
rs11656556	0.81[ASN][1000 genomes]
rs11657908	0.87[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap]
rs11658222	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11868785	0.88[CEU][hapmap];0.95[TSI][hapmap]
rs2014839	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2107540	0.81[ASN][1000 genomes]
rs2251660	0.80[CHB][hapmap];0.87[JPT][hapmap]
rs2280787	0.80[CHB][hapmap];0.87[JPT][hapmap]
rs2280789	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs2306630	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs2376287	0.80[CHB][hapmap];0.87[JPT][hapmap]
rs2526327	0.80[CHB][hapmap];0.87[JPT][hapmap]
rs2526328	0.85[JPT][hapmap]
rs2735475	0.80[CHB][hapmap];0.87[JPT][hapmap]
rs28739295	0.81[ASN][1000 genomes]
rs28912068	0.82[ASN][1000 genomes]
rs3760326	0.86[ASN][1000 genomes]
rs3760447	0.82[ASN][1000 genomes]
rs3785764	1.00[CEU][hapmap];0.88[CHD][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3809769	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.81[ASN][1000 genomes]
rs3817655	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs3817656	0.83[ASN][1000 genomes]
rs3826404	0.82[MEX][hapmap]
rs4251702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4251719	0.88[CEU][hapmap];0.95[TSI][hapmap]
rs4251727	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4251729	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4251751	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4251752	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4251769	0.88[CEU][hapmap];0.95[TSI][hapmap]
rs4251788	0.86[ASN][1000 genomes]
rs4795088	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4795091	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4795092	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4795095	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4795096	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs4795101	0.80[CHB][hapmap];0.87[JPT][hapmap]
rs4796107	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4796108	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4796109	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4796112	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4796113	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4796114	0.88[CEU][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4796115	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4796118	0.86[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.86[ASN][1000 genomes]
rs4796119	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs4796120	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs4796123	0.88[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.81[TSI][hapmap]
rs4796124	0.81[ASN][1000 genomes]
rs4796125	0.81[ASN][1000 genomes]
rs4796136	0.80[CHB][hapmap];0.87[JPT][hapmap]
rs4796138	0.80[CHB][hapmap];0.87[JPT][hapmap]
rs59247105	0.85[ASN][1000 genomes]
rs59338510	0.81[ASN][1000 genomes]
rs7213636	0.87[JPT][hapmap]
rs9303691	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.85[ASN][1000 genomes]
rs9303692	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs9754	0.87[JPT][hapmap]
rs9789051	0.81[ASN][1000 genomes]
rs9889274	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[TSI][hapmap]
rs9889874	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs9894083	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9898132	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs9898152	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.85[ASN][1000 genomes]
rs9899866	0.87[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs9899870	0.87[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap]
rs9900236	0.87[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap]
rs9900473	0.86[ASN][1000 genomes]
rs9904675	0.87[CEU][hapmap];0.92[CHB][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap]
rs9907121	0.86[ASN][1000 genomes]
rs9907295	0.87[CEU][hapmap];0.93[CHB][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap]
rs9907588	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9908011	0.87[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap]
rs9908907	0.83[ASN][1000 genomes]
rs9909050	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs9911598	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9912284	0.86[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap]
rs9912552	0.83[ASN][1000 genomes]
rs9912571	0.86[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap]
rs9912793	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs9913488	0.87[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap]
rs9913559	0.80[CHB][hapmap];0.87[JPT][hapmap]
rs9914401	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.85[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4795089	RDM1	Cis_1M	lymphoblastoid	RTeQTL
rs4795089	TAF15	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:34106000-34121400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr17:34112200-34121800	Weak transcription	Pancreas	Pancrea
3	chr17:34116200-34120200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr17:34116200-34120200	Weak transcription	Esophagus	oesophagus
5	chr17:34116200-34120400	Weak transcription	Lung	lung
6	chr17:34116400-34120200	Enhancers	Hela-S3	cervix
7	chr17:34116400-34121600	Weak transcription	Gastric	stomach
8	chr17:34116600-34119800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr17:34116800-34120200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr17:34116800-34120200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr17:34117200-34120400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr17:34117200-34120600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr17:34117600-34120200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr17:34117600-34120200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr17:34118000-34119600	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr17:34118000-34120200	Weak transcription	Stomach Mucosa	stomach
17	chr17:34118200-34120200	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr17:34118600-34119400	Enhancers	Stomach Smooth Muscle	stomach
19	chr17:34118600-34120200	Enhancers	Rectal Smooth Muscle	rectum
20	chr17:34118800-34119600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr17:34118800-34120200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr17:34118800-34121400	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr17:34118800-34121800	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr17:34119000-34119400	ZNF genes & repeats	Adipose Nuclei	Adipose
25	chr17:34119000-34119400	Enhancers	Brain Substantia Nigra	brain
26	chr17:34119000-34119400	Enhancers	Right Ventricle	heart
27	chr17:34119000-34119600	Enhancers	Right Atrium	heart
28	chr17:34119000-34119600	Flanking Active TSS	HMEC	breast
29	chr17:34119000-34120400	Weak transcription	A549	lung
30	chr17:34119000-34120800	Flanking Active TSS	NHEK	skin
31	chr17:34119000-34121000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr17:34119200-34119400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr17:34119200-34120000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr17:34119200-34120400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr17:34119200-34120400	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr17:34119200-34121000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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