Variant report

Variant	rs9646193
Chromosome Location	chr15:41956469-41956470
allele	C/T
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	chr15:41956109-41956531	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:41894665..41896656-chr15:41956346..41957868,2	K562	blood:
2	chr15:41953002..41954579-chr15:41954789..41956484,2	MCF-7	breast:
3	chr15:41953663..41957556-chr15:41966682..41969969,3	K562	blood:
4	chr15:41954590..41956853-chr15:41972603..41974738,2	K562	blood:

Variant related genes	Relation type
MGA	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1122884	0.91[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap]
rs11630972	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631051	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11632519	1.00[JPT][hapmap]
rs11633160	0.85[EUR][1000 genomes]
rs11634083	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs11634582	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs11634804	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11636523	0.87[ASW][hapmap];0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs1197667	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs1197669	0.91[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap]
rs1197671	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs1197672	0.96[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap]
rs1197703	0.91[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap]
rs1197705	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs12148570	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906666	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12917387	0.95[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17676332	1.00[JPT][hapmap]
rs17677098	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17677757	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17678310	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs2178003	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs2925339	0.96[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs34040639	1.00[JPT][hapmap]
rs34621600	0.95[EUR][1000 genomes]
rs35665813	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35714979	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61104950	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62003901	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167078	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175318	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040094	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042809	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs890503	0.81[TSI][hapmap]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9646193	SPTBN5	cis	cerebellum	SCAN
rs9646193	RPAP1	cis	parietal	SCAN
rs9646193	MAPKBP1	cis	parietal	SCAN
rs9646193	MAPKBP1	cis	cerebellum	SCAN
rs9646193	CAPN3	cis	parietal	SCAN
rs9646193	SNAP23	cis	parietal	SCAN
rs9646193	NDUFAF1	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41954200-41962600	Weak transcription	Spleen	Spleen
2	chr15:41954400-41961600	Weak transcription	Gastric	stomach
3	chr15:41954400-41964600	Weak transcription	Lung	lung
4	chr15:41954400-41970600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:41954400-41978600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:41954400-41982800	Weak transcription	Small Intestine	intestine
7	chr15:41954600-41957400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:41954600-41957400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:41954600-41957600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:41954600-41957600	Weak transcription	Pancreas	Pancrea
11	chr15:41954600-41958200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:41954600-41958400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:41954600-41958400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:41954600-41958600	Weak transcription	NHLF	lung
15	chr15:41954600-41958800	Weak transcription	Colon Smooth Muscle	Colon
16	chr15:41954600-41960400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr15:41954600-41961000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:41954600-41961000	Weak transcription	Fetal Thymus	thymus
19	chr15:41954600-41961200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:41954600-41961200	Weak transcription	Aorta	Aorta
21	chr15:41954600-41961200	Weak transcription	Fetal Muscle Leg	muscle
22	chr15:41954600-41961400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:41954600-41961400	Weak transcription	Ovary	ovary
24	chr15:41954600-41961600	Weak transcription	Esophagus	oesophagus
25	chr15:41954600-41961600	Weak transcription	Placenta	Placenta
26	chr15:41954600-41961600	Weak transcription	Right Atrium	heart
27	chr15:41954600-41961600	Weak transcription	Right Ventricle	heart
28	chr15:41954600-41961800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr15:41954600-41964000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr15:41954600-41964000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:41954600-41964200	Weak transcription	Fetal Stomach	stomach
32	chr15:41954600-41964800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:41954600-41965600	Weak transcription	Left Ventricle	heart
34	chr15:41954600-41976200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr15:41954600-41983800	Weak transcription	Thymus	Thymus
36	chr15:41954600-42001000	Weak transcription	Colonic Mucosa	Colon
37	chr15:41954800-41956600	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr15:41954800-41956800	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr15:41954800-41957000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:41954800-41958200	Weak transcription	NH-A	brain
41	chr15:41954800-41958400	Weak transcription	HSMM	muscle
42	chr15:41954800-41958400	Weak transcription	NHDF-Ad	bronchial
43	chr15:41954800-41958400	Weak transcription	NHEK	skin
44	chr15:41954800-41958400	Weak transcription	Osteobl	bone
45	chr15:41954800-41958600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr15:41954800-41958800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:41954800-41960000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr15:41954800-41961000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr15:41954800-41961000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr15:41954800-41961000	Weak transcription	Primary T cells from cord blood	blood

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