Variant report

Variant	rs6505496
Chromosome Location	chr17:34129067-34129068
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:34121512..34124948-chr17:34126403..34130533,5	K562	blood:
2	chr17:34121512..34125542-chr17:34125807..34130533,7	K562	blood:
3	chr17:34107060..34109022-chr17:34127113..34129378,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000129270	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11650668	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11653282	0.91[JPT][hapmap]
rs11868785	0.80[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1994182	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs2107538	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];0.84[TSI][hapmap]
rs2251660	0.86[GIH][hapmap];0.96[TSI][hapmap]
rs2280789	0.80[CEU][hapmap];0.95[JPT][hapmap]
rs2291299	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]
rs2306630	0.80[CEU][hapmap];0.95[JPT][hapmap]
rs2526327	0.86[GIH][hapmap];0.96[TSI][hapmap]
rs2735475	0.86[GIH][hapmap];0.96[TSI][hapmap]
rs28595279	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35517765	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3760327	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3817655	0.89[ASW][hapmap];0.80[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes]
rs3826404	0.83[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs4079183	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4239252	0.85[EUR][1000 genomes]
rs4251703	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4251710	0.90[LWK][hapmap]
rs4251719	0.80[CEU][hapmap];0.95[JPT][hapmap]
rs4251724	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4251749	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4251769	0.80[CEU][hapmap];0.95[JPT][hapmap]
rs4251787	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4251791	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4325615	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4795087	0.86[EUR][1000 genomes]
rs4795090	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4795096	0.80[CEU][hapmap];0.95[JPT][hapmap]
rs4796105	0.91[CEU][hapmap];0.92[TSI][hapmap]
rs4796116	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4796123	0.80[CEU][hapmap];0.84[MEX][hapmap]
rs4796128	0.89[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs4796138	0.86[GIH][hapmap];0.96[TSI][hapmap]
rs55858632	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6505498	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7215845	0.81[EUR][1000 genomes]
rs8066406	0.80[EUR][1000 genomes]
rs8080959	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9303692	0.80[CEU][hapmap];0.95[JPT][hapmap]
rs9754	0.86[GIH][hapmap];0.96[TSI][hapmap]
rs9889874	0.80[CEU][hapmap];0.95[JPT][hapmap]
rs9908928	0.84[EUR][1000 genomes]
rs9909416	0.84[JPT][hapmap]
rs9913559	0.81[GIH][hapmap]

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6505496	RDM1	cis	Lymphoblastoid	GTEx
rs6505496	C17orf50	cis	cerebellum	SCAN
rs6505496	RDM1	cis	parietal	SCAN
rs6505496	RDM1	cis	lymphoblastoid	seeQTL
rs6505496	RDM1	Cis_1M	lymphoblastoid	RTeQTL
rs6505496	CCL5	cis	Lymphoblastoid	GTEx
rs6505496	AMAC1	cis	cerebellum	SCAN
rs6505496	RAD52B	cis	multi-tissue	Pritchard
rs6505496	TAF15	Cis_1M	lymphoblastoid	RTeQTL
rs6505496	CCL5	cis	lymphoblastoid	seeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:34125600-34129400	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr17:34126200-34129200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr17:34126200-34129200	Enhancers	Fetal Heart	heart
4	chr17:34126400-34129200	Enhancers	Colon Smooth Muscle	Colon
5	chr17:34126400-34129200	Enhancers	Rectal Smooth Muscle	rectum
6	chr17:34126600-34129200	Enhancers	Adipose Nuclei	Adipose
7	chr17:34126600-34129200	Enhancers	Brain Anterior Caudate	brain
8	chr17:34126600-34129200	Enhancers	Brain Germinal Matrix	brain
9	chr17:34126600-34129200	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr17:34126600-34129200	Enhancers	Fetal Brain Male	brain
11	chr17:34126600-34129200	Enhancers	Fetal Muscle Leg	muscle
12	chr17:34126600-34129200	Enhancers	Fetal Stomach	stomach
13	chr17:34126600-34129200	Enhancers	HSMMtube	muscle
14	chr17:34126800-34129200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr17:34126800-34129200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr17:34126800-34129200	Enhancers	Brain Substantia Nigra	brain
17	chr17:34126800-34129200	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr17:34126800-34130800	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr17:34126800-34132000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr17:34127000-34129200	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr17:34127000-34129200	Enhancers	Colonic Mucosa	Colon
22	chr17:34127000-34129200	Enhancers	Esophagus	oesophagus
23	chr17:34127000-34129200	Enhancers	Left Ventricle	heart
24	chr17:34127000-34129400	Enhancers	Lung	lung
25	chr17:34127000-34130000	Enhancers	Primary hematopoietic stem cells	blood
26	chr17:34127000-34135400	Weak transcription	Liver	Liver
27	chr17:34127200-34129200	Enhancers	Placenta	Placenta
28	chr17:34127200-34130200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr17:34127200-34135000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr17:34127400-34129200	Enhancers	Primary B cells from peripheral blood	blood
31	chr17:34127400-34129200	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr17:34127600-34129200	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr17:34127600-34135800	Weak transcription	Aorta	Aorta
34	chr17:34127800-34129400	Enhancers	Fetal Thymus	thymus
35	chr17:34127800-34131600	Weak transcription	A549	lung
36	chr17:34127800-34131600	Weak transcription	Hela-S3	cervix
37	chr17:34127800-34134000	Weak transcription	NHEK	skin
38	chr17:34128200-34129200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr17:34128200-34129200	Enhancers	Primary T cells from cord blood	blood
40	chr17:34128200-34129200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr17:34128200-34129200	Enhancers	Stomach Mucosa	stomach
42	chr17:34128200-34129200	Enhancers	Thymus	Thymus
43	chr17:34128400-34129200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr17:34128400-34129200	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr17:34128400-34129200	Enhancers	Dnd41	blood
46	chr17:34128400-34129200	Flanking Active TSS	HUVEC	blood vessel
47	chr17:34128600-34129200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr17:34128600-34129200	Enhancers	K562	blood
49	chr17:34128800-34129200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr17:34128800-34129200	Flanking Active TSS	Fetal Brain Female	brain

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