Variant report

Variant	rs9535652
Chromosome Location	chr13:51945741-51945742
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:51945578-51946085	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:51938430..51941174-chr13:51944104..51948197,3	MCF-7	breast:

Variant related genes	Relation type
INTS6	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1028727	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12860899	1.00[LWK][hapmap]
rs17194948	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17195020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2026526	0.80[ASN][1000 genomes]
rs2277443	1.00[ASW][hapmap];0.80[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap]
rs2408363	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4628860	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4943003	1.00[ASW][hapmap]
rs56017742	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6561638	1.00[ASW][hapmap]
rs73197809	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73197821	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73197824	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7321642	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7328715	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7335122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7335144	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7337450	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7989850	0.90[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7998084	0.90[CEU][hapmap]
rs9316541	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];0.90[ASN][1000 genomes]
rs9316545	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9316546	0.80[ASN][1000 genomes]
rs9526757	0.90[CEU][hapmap];0.95[EUR][1000 genomes]
rs9526758	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526759	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526761	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526764	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535625	1.00[LWK][hapmap]
rs9535640	0.85[EUR][1000 genomes]
rs9535644	0.81[EUR][1000 genomes]
rs9535646	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535655	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535661	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]
rs9535662	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535663	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[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];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535665	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535670	0.90[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535671	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535678	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535682	0.88[ASN][1000 genomes]
rs9535683	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9535694	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9535696	0.89[CEU][hapmap]
rs9535697	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs9535699	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9563046	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568600	0.89[CEU][hapmap]
rs9568603	0.90[CEU][hapmap];0.80[TSI][hapmap]
rs9568612	0.90[CEU][hapmap];0.85[CHB][hapmap]
rs9634842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9535652	CKAP2	cis	parietal	SCAN
rs9535652	ITM2B	cis	cerebellum	SCAN
rs9535652	DDX26	cis	multi-tissue	Pritchard
rs9535652	WDFY2	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51932000-51945800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr13:51932000-51947400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr13:51933600-51947600	Weak transcription	Brain Substantia Nigra	brain
4	chr13:51933800-51947400	Weak transcription	Brain Germinal Matrix	brain
5	chr13:51934000-51947000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr13:51934200-51958400	Strong transcription	Placenta	Placenta
7	chr13:51934200-51959800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr13:51934400-51945800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr13:51934400-51947400	Weak transcription	Psoas Muscle	Psoas
10	chr13:51934400-51963800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr13:51934600-51946200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr13:51934600-51955800	Weak transcription	Fetal Intestine Small	intestine
13	chr13:51935000-51949400	Weak transcription	Colonic Mucosa	Colon
14	chr13:51935400-51957800	Strong transcription	Fetal Thymus	thymus
15	chr13:51935400-51959600	Strong transcription	GM12878-XiMat	blood
16	chr13:51935600-51954000	Weak transcription	Stomach Mucosa	stomach
17	chr13:51935600-51971400	Weak transcription	Gastric	stomach
18	chr13:51935800-51954800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr13:51935800-51962000	Strong transcription	Dnd41	blood
20	chr13:51936000-51947600	Weak transcription	Small Intestine	intestine
21	chr13:51936200-51963600	Strong transcription	Liver	Liver
22	chr13:51936400-51966000	Weak transcription	Right Ventricle	heart
23	chr13:51937000-51949800	Weak transcription	Fetal Brain Male	brain
24	chr13:51937400-51953200	Strong transcription	Fetal Intestine Large	intestine
25	chr13:51937400-51961800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr13:51937600-51947400	Weak transcription	K562	blood
27	chr13:51937600-51954400	Weak transcription	Fetal Heart	heart
28	chr13:51938200-51960000	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr13:51938400-51959200	Strong transcription	Primary B cells from peripheral blood	blood
30	chr13:51938400-51959600	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr13:51938600-51952200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr13:51938600-51959400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr13:51938600-51960400	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr13:51938600-51961800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr13:51938800-51954400	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr13:51939200-51947600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr13:51939200-51949000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr13:51939200-51954400	Strong transcription	HMEC	breast
39	chr13:51939200-51954600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr13:51939200-51970600	Weak transcription	Brain Angular Gyrus	brain
41	chr13:51939400-51962200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr13:51940200-51950000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr13:51940200-51954600	Strong transcription	Primary hematopoietic stem cells	blood
44	chr13:51940400-51958000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr13:51940400-51959200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr13:51940600-51952600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr13:51940800-51947800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr13:51941000-51949200	Strong transcription	Primary T cells from cord blood	blood
49	chr13:51941000-51949400	Strong transcription	Fetal Muscle Leg	muscle
50	chr13:51941200-51948600	Strong transcription	Brain Anterior Caudate	brain

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