Variant report

Variant	rs4795090
Chromosome Location	chr17:34123597-34123598
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:34121885..34124383-chr17:34134953..34137697,3	MCF-7	breast:
2	chr17:34113865..34115721-chr17:34122812..34125155,2	MCF-7	breast:
3	chr17:34123180..34125521-chr17:34136848..34139147,2	K562	blood:
4	chr17:34121741..34124084-chr17:34135458..34137103,2	MCF-7	breast:
5	chr17:34113403..34117361-chr17:34123102..34125354,3	K562	blood:
6	chr17:34122737..34124680-chr17:34137626..34139147,2	K562	blood:
7	chr17:34106307..34108184-chr17:34123569..34126227,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172660	Chromatin interaction
ENSG00000267578	Chromatin interaction
ENSG00000129270	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11650668	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11653282	0.91[JPT][hapmap]
rs11868785	0.81[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1994182	0.91[CEU][hapmap];0.82[TSI][hapmap]
rs2107538	0.89[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap]
rs2251660	0.86[GIH][hapmap];0.96[TSI][hapmap]
rs2280789	0.95[JPT][hapmap]
rs2291299	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]
rs2306630	0.95[JPT][hapmap]
rs2526327	0.86[GIH][hapmap];0.96[TSI][hapmap]
rs2735475	0.86[GIH][hapmap];0.96[TSI][hapmap]
rs28595279	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35517765	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3760327	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3817655	0.89[ASW][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes]
rs3826404	0.91[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs4079183	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4239252	0.85[EUR][1000 genomes]
rs4251703	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4251710	0.90[LWK][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs4251719	0.95[JPT][hapmap]
rs4251724	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4251749	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4251769	0.95[JPT][hapmap]
rs4251787	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4251791	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4325615	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4795087	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4795096	0.95[JPT][hapmap]
rs4796105	1.00[CEU][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs4796116	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4796123	0.84[MEX][hapmap]
rs4796128	0.89[ASW][hapmap];0.91[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];0.80[EUR][1000 genomes]
rs4796138	0.86[GIH][hapmap];0.96[TSI][hapmap]
rs55858632	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6505496	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]
rs6505498	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7215845	0.80[EUR][1000 genomes]
rs8080959	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9303692	0.95[JPT][hapmap]
rs9754	0.86[GIH][hapmap];0.96[TSI][hapmap]
rs9889874	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
rs4795090	RDM1	cis	Lymphoblastoid	GTEx
rs4795090	TAF15	Cis_1M	lymphoblastoid	RTeQTL
rs4795090	CCL5	cis	lymphoblastoid	seeQTL
rs4795090	AMAC1	cis	cerebellum	SCAN
rs4795090	RDM1	cis	lymphoblastoid	seeQTL
rs4795090	C17orf50	cis	cerebellum	SCAN
rs4795090	RDM1	cis	parietal	SCAN
rs4795090	RAD52B	cis	multi-tissue	Pritchard
rs4795090	CCL5	cis	Lymphoblastoid	GTEx
rs4795090	RDM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:34123000-34123600	Enhancers	Primary hematopoietic stem cells	blood
2	chr17:34123000-34123600	Bivalent Enhancer	Stomach Mucosa	stomach
3	chr17:34123000-34123600	Enhancers	HSMMtube	muscle
4	chr17:34123000-34126800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr17:34123000-34127000	Weak transcription	Lung	lung
6	chr17:34123000-34127000	Weak transcription	Right Atrium	heart
7	chr17:34123000-34127000	Weak transcription	Spleen	Spleen
8	chr17:34123000-34127200	Weak transcription	Aorta	Aorta
9	chr17:34123200-34123600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr17:34123200-34123600	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr17:34123200-34123600	Enhancers	Hela-S3	cervix
12	chr17:34123200-34123600	Enhancers	HMEC	breast
13	chr17:34123200-34124000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr17:34123200-34124800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr17:34123200-34124800	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr17:34123200-34126200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr17:34123200-34126400	Weak transcription	Colon Smooth Muscle	Colon
18	chr17:34123200-34126800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr17:34123200-34126800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr17:34123200-34127000	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr17:34123200-34127000	Weak transcription	Left Ventricle	heart
22	chr17:34123200-34127200	Weak transcription	Right Ventricle	heart
23	chr17:34123400-34123600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr17:34123400-34124400	Weak transcription	NHEK	skin
25	chr17:34123400-34126200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr17:34123400-34126600	Weak transcription	Adipose Nuclei	Adipose
27	chr17:34123400-34126600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr17:34123400-34127000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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