Variant report

Variant	rs2291299
Chromosome Location	chr17:34191406-34191407
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:34191000..34193680-chr17:34217468..34219346,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TAF15-3	chr17:34190940-34191616	NONHSAT053127

Extended variants
information (count: 72 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs11650409	0.85[MEX][hapmap]
rs11650668	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11653051	0.85[MEX][hapmap]
rs11653282	0.85[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.88[ASN][1000 genomes]
rs11655533	0.85[MEX][hapmap]
rs11657908	0.80[MEX][hapmap]
rs11868244	0.88[ASN][1000 genomes]
rs11868785	0.80[CEU][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs1994182	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs2107538	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2251660	0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs2280787	0.81[EUR][1000 genomes]
rs2280789	0.80[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[ASN][1000 genomes]
rs2306630	0.80[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[ASN][1000 genomes]
rs2376287	0.81[EUR][1000 genomes]
rs2526327	0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs2735475	0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs28595279	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28722787	0.81[EUR][1000 genomes]
rs3760327	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3809769	0.85[MEX][hapmap]
rs3817655	1.00[ASW][hapmap];0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3826404	0.83[CEU][hapmap];0.80[CHB][hapmap];0.93[TSI][hapmap]
rs4079183	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4239252	0.95[EUR][1000 genomes]
rs4251703	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4251710	0.92[LWK][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs4251719	0.80[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[ASN][1000 genomes]
rs4251724	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4251737	0.87[ASN][1000 genomes]
rs4251749	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4251769	0.80[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[ASN][1000 genomes]
rs4251787	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4251791	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4325615	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4795087	0.83[CHB][hapmap]
rs4795090	0.89[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.84[EUR][1000 genomes]
rs4795093	0.92[ASN][1000 genomes]
rs4795096	0.80[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[ASN][1000 genomes]
rs4796105	0.91[CEU][hapmap];0.92[TSI][hapmap]
rs4796112	0.85[MEX][hapmap]
rs4796116	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4796123	0.80[CEU][hapmap]
rs4796128	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4796133	0.81[EUR][1000 genomes]
rs4796134	0.81[EUR][1000 genomes]
rs4796136	0.81[EUR][1000 genomes]
rs4796137	0.81[EUR][1000 genomes]
rs4796138	0.96[TSI][hapmap]
rs55950249	0.85[ASN][1000 genomes]
rs6505496	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes]
rs6505498	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7211393	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7213636	0.81[EUR][1000 genomes]
rs7215845	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8066406	0.88[EUR][1000 genomes]
rs8069014	0.98[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8080959	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9303691	0.85[MEX][hapmap]
rs9303692	0.80[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[ASN][1000 genomes]
rs9754	0.96[TSI][hapmap]
rs9889874	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]
rs9890583	0.81[EUR][1000 genomes]
rs9898152	0.85[MEX][hapmap]
rs9899881	0.81[EUR][1000 genomes]
rs9900563	0.87[ASN][1000 genomes]
rs9908011	0.84[MEX][hapmap]
rs9908928	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9909416	0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs9913488	0.84[MEX][hapmap]
rs9913559	0.81[EUR][1000 genomes]
rs9914401	0.85[MEX][hapmap]

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2291299	AMAC1	cis	cerebellum	SCAN
rs2291299	TAF15	Cis_1M	lymphoblastoid	RTeQTL
rs2291299	C17orf50	cis	cerebellum	SCAN
rs2291299	RDM1	cis	parietal	SCAN
rs2291299	TAF15	cis	normal skin	skin_eQTL
rs2291299	RDM1	cis	Lymphoblastoid	GTEx
rs2291299	CCL5	cis	Lymphoblastoid	GTEx
rs2291299	CCL5	cis	lymphoblastoid	seeQTL
rs2291299	RDM1	cis	multi-tissue	Pritchard
rs2291299	RDM1	Cis_1M	lymphoblastoid	RTeQTL
rs2291299	RDM1	cis	lymphoblastoid	seeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:34170200-34192800	Weak transcription	Small Intestine	intestine
2	chr17:34172200-34193600	Weak transcription	Right Ventricle	heart
3	chr17:34172800-34193600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr17:34175400-34192200	Weak transcription	Gastric	stomach
5	chr17:34175600-34193000	Weak transcription	NH-A	brain
6	chr17:34175600-34193600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr17:34175600-34202400	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr17:34176400-34192600	Weak transcription	Fetal Intestine Small	intestine
9	chr17:34176800-34193200	Weak transcription	Fetal Brain Female	brain
10	chr17:34177200-34202400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr17:34177400-34192200	Weak transcription	Lung	lung
12	chr17:34177400-34193000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr17:34177400-34193200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr17:34177400-34193200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr17:34177400-34193200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr17:34177400-34198400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr17:34177800-34198200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr17:34178000-34193600	Weak transcription	Left Ventricle	heart
19	chr17:34178200-34193200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr17:34179000-34193400	Weak transcription	Osteobl	bone
21	chr17:34179000-34203800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr17:34180200-34193400	Weak transcription	HUVEC	blood vessel
23	chr17:34180400-34192400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr17:34180600-34198200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr17:34180800-34202000	Weak transcription	GM12878-XiMat	blood
26	chr17:34182800-34191600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr17:34182800-34192800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr17:34182800-34193000	Weak transcription	HSMMtube	muscle
29	chr17:34183800-34191600	Weak transcription	Thymus	Thymus
30	chr17:34183800-34192600	Weak transcription	Esophagus	oesophagus
31	chr17:34183800-34192600	Weak transcription	NHLF	lung
32	chr17:34183800-34193000	Weak transcription	A549	lung
33	chr17:34183800-34193400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr17:34183800-34193400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr17:34183800-34193600	Weak transcription	Aorta	Aorta
36	chr17:34183800-34198200	Weak transcription	Pancreas	Pancrea
37	chr17:34184000-34191800	Weak transcription	Fetal Thymus	thymus
38	chr17:34184000-34192200	Weak transcription	Fetal Intestine Large	intestine
39	chr17:34184000-34192800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr17:34184000-34192800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr17:34184000-34193200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr17:34184200-34192800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr17:34184200-34192800	Weak transcription	Brain Germinal Matrix	brain
44	chr17:34184200-34193000	Weak transcription	HSMM	muscle
45	chr17:34184400-34193000	Weak transcription	Brain Hippocampus Middle	brain
46	chr17:34184400-34193200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr17:34184400-34193400	Weak transcription	Placenta	Placenta
48	chr17:34184600-34192600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr17:34184600-34192800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr17:34184600-34193400	Weak transcription	Fetal Stomach	stomach

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