Variant report

Variant	rs17238601
Chromosome Location	chr15:56394295-56394296
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:56393395..56396114-chr15:56404185..56407853,3	MCF-7	breast:
2	chr15:56389724..56392498-chr15:56393728..56396342,2	K562	blood:
3	chr15:56389724..56392748-chr15:56393728..56397126,3	K562	blood:
4	chr15:56379651..56381726-chr15:56393223..56394783,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10152826	0.88[CEU][hapmap];0.92[JPT][hapmap]
rs10162834	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10163161	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11632218	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11858173	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11858245	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12899534	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12909153	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13379820	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17819384	0.88[LWK][hapmap]
rs1829543	1.00[CEU][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs2247838	0.80[EUR][1000 genomes]
rs2414466	0.82[CEU][hapmap]
rs2460649	0.96[CEU][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap]
rs2465405	0.82[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes]
rs2584689	1.00[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2682030	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2682031	1.00[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs2682032	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2682048	0.82[AMR][1000 genomes]
rs2682050	1.00[JPT][hapmap];0.92[LWK][hapmap];0.90[YRI][hapmap]
rs2682055	0.84[AMR][1000 genomes]
rs2713922	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2713934	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2713937	1.00[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs2713939	0.82[EUR][1000 genomes]
rs2718924	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2725871	1.00[JPT][hapmap]
rs2947023	0.82[EUR][1000 genomes]
rs34361729	0.83[ASN][1000 genomes]
rs35840822	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56274791	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60138831	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62044114	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6493836	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7170102	0.89[EUR][1000 genomes]
rs748344	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8041422	0.88[CEU][hapmap];0.92[JPT][hapmap];0.82[TSI][hapmap]
rs894415	1.00[CEU][hapmap];0.94[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761872	chr15:56211065-56426501	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv833018	chr15:56325799-56492535	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1045906	chr15:56333180-56473614	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17238601	RFXDC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56381600-56397000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:56382200-56399200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:56382800-56395800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr15:56383200-56395600	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr15:56383400-56395200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:56383800-56398400	Strong transcription	Dnd41	blood
7	chr15:56384000-56395800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr15:56384600-56395000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:56385000-56394800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:56385600-56394400	Strong transcription	Liver	Liver
11	chr15:56385600-56394800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr15:56385600-56405600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:56386200-56395000	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr15:56386400-56397400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr15:56386600-56396200	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr15:56387400-56396000	Weak transcription	Fetal Heart	heart
17	chr15:56388400-56402000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr15:56388800-56396000	Weak transcription	Colonic Mucosa	Colon
19	chr15:56388800-56396200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr15:56388800-56396400	Weak transcription	Gastric	stomach
21	chr15:56388800-56396400	Weak transcription	Right Ventricle	heart
22	chr15:56388800-56396600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:56388800-56397400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr15:56388800-56398400	Weak transcription	Esophagus	oesophagus
25	chr15:56388800-56399000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr15:56388800-56399200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:56388800-56400600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr15:56388800-56403400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:56388800-56411600	Weak transcription	Fetal Stomach	stomach
30	chr15:56388800-56414400	Weak transcription	Thymus	Thymus
31	chr15:56388800-56418400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr15:56388800-56433000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:56388800-56437200	Weak transcription	Pancreas	Pancrea
34	chr15:56388800-56441600	Weak transcription	Lung	lung
35	chr15:56389000-56394800	Weak transcription	Fetal Brain Female	brain
36	chr15:56389000-56397200	Weak transcription	Hela-S3	cervix
37	chr15:56389000-56398400	Weak transcription	K562	blood
38	chr15:56389200-56395200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr15:56389200-56396600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:56389400-56395400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr15:56389400-56395600	Weak transcription	Brain Germinal Matrix	brain
42	chr15:56389400-56397200	Weak transcription	Fetal Kidney	kidney
43	chr15:56389400-56407600	Weak transcription	Brain Substantia Nigra	brain
44	chr15:56389400-56418400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr15:56389400-56418400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr15:56389600-56395000	Weak transcription	NHLF	lung
47	chr15:56389600-56395600	Weak transcription	Brain Anterior Caudate	brain
48	chr15:56389600-56402000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr15:56389600-56414400	Weak transcription	HSMMtube	muscle
50	chr15:56389800-56415600	Weak transcription	Placenta	Placenta

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