Variant report

Variant	rs9889874
Chromosome Location	chr17:34202297-34202298
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:34200979..34203513-chr17:34206991..34209447,2	K562	blood:
2	chr17:34136067..34137819-chr17:34202114..34205071,2	K562	blood:

Variant related genes	Relation type
ENSG00000161570	Chromatin interaction
ENSG00000172660	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs11080359	0.80[TSI][hapmap]
rs11080360	0.81[EUR][1000 genomes]
rs11080361	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11080362	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11650409	0.89[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11650668	0.84[ASN][1000 genomes]
rs11652536	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11653016	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11653051	0.89[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11653204	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11653282	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11655533	0.89[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11656556	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11657908	0.89[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11868244	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11868785	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]
rs11868801	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16971670	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2014839	0.82[AFR][1000 genomes]
rs2107538	0.80[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2107540	0.85[EUR][1000 genomes]
rs2280789	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2291299	0.80[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[ASN][1000 genomes]
rs2306630	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28550999	0.85[EUR][1000 genomes]
rs28595279	0.88[ASN][1000 genomes]
rs28739295	0.85[EUR][1000 genomes]
rs28912068	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3760326	0.85[EUR][1000 genomes]
rs3760327	0.91[ASN][1000 genomes]
rs3760447	0.81[AMR][1000 genomes]
rs3785764	1.00[CEU][hapmap];0.82[TSI][hapmap]
rs3809769	0.88[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3817655	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3817656	0.87[EUR][1000 genomes]
rs4079183	0.91[ASN][1000 genomes]
rs4251702	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs4251703	0.90[JPT][hapmap]
rs4251719	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[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];0.89[ASN][1000 genomes]
rs4251724	0.95[JPT][hapmap]
rs4251737	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4251749	0.86[ASN][1000 genomes]
rs4251751	0.88[CEU][hapmap]
rs4251752	0.88[CEU][hapmap]
rs4251769	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4251787	0.91[ASN][1000 genomes]
rs4251788	0.85[EUR][1000 genomes]
rs4251791	0.86[ASN][1000 genomes]
rs4325615	0.88[ASN][1000 genomes]
rs4795087	0.81[CHB][hapmap]
rs4795089	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs4795090	0.95[JPT][hapmap]
rs4795093	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4795095	0.88[CEU][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4795096	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4795097	0.81[EUR][1000 genomes]
rs4795099	0.82[AMR][1000 genomes]
rs4795100	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4796107	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs4796108	0.86[CEU][hapmap]
rs4796112	0.92[ASW][hapmap];0.88[CEU][hapmap];0.89[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes]
rs4796115	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs4796116	0.89[ASN][1000 genomes]
rs4796118	0.84[ASW][hapmap];0.89[GIH][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4796119	0.87[CEU][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs4796120	0.88[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs4796123	1.00[CEU][hapmap];0.84[GIH][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4796124	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4796125	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4796126	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4796127	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4796128	0.80[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.91[ASN][1000 genomes]
rs4796129	0.85[EUR][1000 genomes]
rs4796130	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4796131	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55950249	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56294660	0.85[EUR][1000 genomes]
rs56344830	0.83[EUR][1000 genomes]
rs59247105	0.87[EUR][1000 genomes]
rs59338510	0.82[EUR][1000 genomes]
rs6505496	0.80[CEU][hapmap];0.95[JPT][hapmap]
rs7211393	0.93[ASN][1000 genomes]
rs7215845	0.88[ASN][1000 genomes]
rs8069014	0.85[ASN][1000 genomes]
rs8080959	0.84[ASN][1000 genomes]
rs9303691	0.92[ASW][hapmap];0.88[CEU][hapmap];0.89[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9303692	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9303693	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9789051	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9889274	0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs9889977	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9891064	0.81[EUR][1000 genomes]
rs9893004	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9894083	0.83[EUR][1000 genomes]
rs9894314	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9894799	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9896265	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9896658	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9897665	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9898132	0.88[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs9898152	0.92[ASW][hapmap];0.88[CEU][hapmap];0.89[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9899215	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9899866	0.89[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs9899870	0.81[EUR][1000 genomes]
rs9900236	0.89[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9900563	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9901195	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9901418	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9903590	0.85[AMR][1000 genomes]
rs9904675	0.89[GIH][hapmap];0.95[TSI][hapmap]
rs9907121	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9907145	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9907295	0.89[GIH][hapmap];0.95[TSI][hapmap]
rs9907588	0.82[EUR][1000 genomes]
rs9908011	0.89[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9908525	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9908907	0.87[EUR][1000 genomes]
rs9908928	0.92[ASN][1000 genomes]
rs9909050	0.88[CEU][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs9909416	0.85[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9911016	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9911598	0.80[AFR][1000 genomes]
rs9912049	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9912284	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9912552	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9912571	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9912793	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9912894	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9913488	0.89[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9914401	0.92[ASW][hapmap];0.88[CEU][hapmap];0.89[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9914468	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9889874	RDM1	Cis_1M	lymphoblastoid	RTeQTL
rs9889874	RDM1	cis	lymphoblastoid	seeQTL
rs9889874	CCL5	cis	lymphoblastoid	seeQTL
rs9889874	RDM1	cis	multi-tissue	Pritchard
rs9889874	TAF15	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:34175600-34202400	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr17:34177200-34202400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr17:34179000-34203800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:34185800-34206800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr17:34192200-34218000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr17:34192400-34213200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr17:34194000-34205800	Weak transcription	K562	blood
8	chr17:34197800-34202400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr17:34198400-34202400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr17:34198400-34205400	Weak transcription	Pancreas	Pancrea
11	chr17:34198600-34202400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr17:34198600-34202400	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr17:34198800-34202400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr17:34198800-34202400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr17:34198800-34202600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr17:34198800-34206800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr17:34198800-34206800	Weak transcription	Placenta	Placenta
18	chr17:34199200-34207200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr17:34199400-34202400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr17:34199400-34202400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr17:34199400-34202600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr17:34199600-34202400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr17:34199600-34202400	Weak transcription	Fetal Thymus	thymus
24	chr17:34199600-34202400	Weak transcription	Spleen	Spleen
25	chr17:34200000-34202600	Weak transcription	Primary T cells from cord blood	blood
26	chr17:34200800-34202400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr17:34201200-34202400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr17:34201400-34204000	Enhancers	HepG2	liver
29	chr17:34201800-34202400	Enhancers	HUVEC	blood vessel
30	chr17:34202000-34202400	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr17:34202000-34203000	Flanking Active TSS	GM12878-XiMat	blood
32	chr17:34202200-34203000	Enhancers	Primary hematopoietic stem cells	blood
33	chr17:34202200-34203800	Enhancers	Adipose Nuclei	Adipose
34	chr17:34202200-34204000	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood

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