Variant report

Variant	rs9535661
Chromosome Location	chr13:51992161-51992162
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:51987238..51991497-chr13:51991664..51994935,3	K562	blood:
2	chr13:51987155..51989233-chr13:51992087..51994561,2	MCF-7	breast:
3	chr13:51990141..51994470-chr13:51996200..51998444,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102786	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1028727	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12860899	1.00[LWK][hapmap]
rs17075688	0.80[EUR][1000 genomes]
rs17194948	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17195020	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2026526	0.82[ASN][1000 genomes]
rs2277443	1.00[ASW][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap]
rs2408363	0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3908968	1.00[ASW][hapmap]
rs4555048	1.00[ASW][hapmap]
rs4628860	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4943003	1.00[ASW][hapmap]
rs56017742	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6561638	1.00[ASW][hapmap]
rs73197809	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73197821	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73197824	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7321642	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7328715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7335122	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7335144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7337450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7989850	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7998084	0.90[CEU][hapmap]
rs8001311	0.80[EUR][1000 genomes]
rs9316541	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9316545	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9316546	0.82[ASN][1000 genomes]
rs9526757	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs9526758	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9526759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9526761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9526764	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535625	1.00[LWK][hapmap]
rs9535640	0.83[EUR][1000 genomes]
rs9535646	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535652	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535660	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535663	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535665	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535670	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535671	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535672	0.80[EUR][1000 genomes]
rs9535677	0.80[EUR][1000 genomes]
rs9535678	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535679	0.80[EUR][1000 genomes]
rs9535680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535682	0.90[ASN][1000 genomes]
rs9535683	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535694	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9535696	0.89[CEU][hapmap]
rs9535697	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs9535699	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9535717	1.00[ASW][hapmap]
rs9563046	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9568600	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs9568603	0.90[CEU][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs9568612	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs9634842	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9535661	DDX26	cis	multi-tissue	Pritchard
rs9535661	ITM2B	cis	cerebellum	SCAN
rs9535661	WDFY2	cis	parietal	SCAN
rs9535661	CKAP2	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51945800-52016600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:51949400-52025000	Weak transcription	Fetal Muscle Leg	muscle
3	chr13:51950000-52025200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr13:51950200-51999800	Weak transcription	Brain Germinal Matrix	brain
5	chr13:51958000-51996800	Weak transcription	Thymus	Thymus
6	chr13:51962200-51993200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr13:51963200-52024800	Weak transcription	Fetal Intestine Large	intestine
8	chr13:51963600-52003600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr13:51969600-51995000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr13:51971800-52025000	Weak transcription	Fetal Stomach	stomach
11	chr13:51972000-51993400	Weak transcription	Stomach Mucosa	stomach
12	chr13:51972000-51995000	Weak transcription	Placenta	Placenta
13	chr13:51972000-51995200	Weak transcription	HSMMtube	muscle
14	chr13:51972000-51996800	Weak transcription	Ovary	ovary
15	chr13:51972000-51999400	Weak transcription	Small Intestine	intestine
16	chr13:51972000-52005200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr13:51972000-52016000	Weak transcription	Pancreas	Pancrea
18	chr13:51972400-51996400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr13:51972600-51993000	Weak transcription	Colon Smooth Muscle	Colon
20	chr13:51973800-51993200	Weak transcription	Hela-S3	cervix
21	chr13:51977000-51996800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr13:51978400-51995200	Weak transcription	Gastric	stomach
23	chr13:51978400-52003200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr13:51980000-51995000	Weak transcription	Brain Substantia Nigra	brain
25	chr13:51981600-51999400	Weak transcription	Brain Angular Gyrus	brain
26	chr13:51983800-51993000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr13:51984400-52024800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr13:51985000-51999400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr13:51985400-51995000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr13:51985600-51992200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr13:51985600-51995200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr13:51985800-51995400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr13:51986400-51996800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr13:51988200-52001000	Weak transcription	Aorta	Aorta
35	chr13:51988400-51993400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr13:51988400-51995200	Weak transcription	Left Ventricle	heart
37	chr13:51988400-51995200	Weak transcription	Right Atrium	heart
38	chr13:51988400-51996600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr13:51988400-51996600	Weak transcription	Psoas Muscle	Psoas
40	chr13:51988600-51993400	Weak transcription	Adipose Nuclei	Adipose
41	chr13:51988600-51999400	Weak transcription	Brain Anterior Caudate	brain
42	chr13:51988600-51999400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr13:51988800-51993000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr13:51988800-51994000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr13:51988800-51999400	Weak transcription	Brain Hippocampus Middle	brain
46	chr13:51988800-52024400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr13:51989000-51992400	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr13:51989000-51992400	ZNF genes & repeats	GM12878-XiMat	blood
49	chr13:51989400-51992200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr13:51989400-51993600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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