Variant report

Variant	rs10238965
Chromosome Location	chr7:99145845-99145846
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99143301..99146119-chr7:99146744..99149736,4	MCF-7	breast:
2	chr7:99145271..99147369-chr7:99155263..99156996,2	K562	blood:
3	chr7:99141181..99143038-chr7:99144864..99146762,2	K562	blood:
4	chr7:99102742..99104293-chr7:99144379..99147325,2	K562	blood:
5	chr7:99140989..99143038-chr7:99144638..99146762,3	K562	blood:
6	chr7:99143100..99146445-chr7:99147648..99150880,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196652	Chromatin interaction
ENSG00000221909	Chromatin interaction
ENSG00000272647	Chromatin interaction
ENSG00000197343	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1011024	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10155966	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs10211	0.83[JPT][hapmap]
rs10225314	0.93[JPT][hapmap]
rs10240199	0.81[ASN][1000 genomes]
rs10242455	0.83[JPT][hapmap]
rs10243678	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs10244158	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10253937	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10254729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10258757	0.91[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap]
rs10265385	0.83[ASN][1000 genomes]
rs10270459	0.92[CEU][hapmap];0.83[JPT][hapmap]
rs10270917	0.92[CEU][hapmap];0.80[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap]
rs10271049	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10271582	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10279308	0.84[CEU][hapmap]
rs10282706	0.83[JPT][hapmap]
rs1043466	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11762273	0.91[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]
rs11772470	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11976018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11978089	0.84[CEU][hapmap]
rs12360	0.84[JPT][hapmap]
rs13227795	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13240600	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13437771	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1357319	0.83[JPT][hapmap]
rs15524	0.83[JPT][hapmap]
rs17161768	0.80[ASN][1000 genomes]
rs17161769	0.80[ASN][1000 genomes]
rs1859690	0.83[JPT][hapmap]
rs1879859	0.84[JPT][hapmap]
rs1980307	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2003499	0.84[CEU][hapmap]
rs2037498	0.84[JPT][hapmap]
rs2037499	0.84[JPT][hapmap]
rs2072181	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap]
rs2222411	0.84[JPT][hapmap]
rs2240384	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2240385	0.85[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap]
rs2257401	0.84[JPT][hapmap]
rs2272168	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280600	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2280601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2286162	0.92[CEU][hapmap]
rs2404324	0.85[EUR][1000 genomes]
rs2404770	0.83[JPT][hapmap]
rs2687076	0.84[JPT][hapmap]
rs2687079	0.84[JPT][hapmap]
rs2687081	0.83[JPT][hapmap]
rs2687086	0.89[JPT][hapmap]
rs2687087	0.84[JPT][hapmap]
rs2687133	0.84[JPT][hapmap]
rs2687134	0.83[JPT][hapmap]
rs2687136	0.84[JPT][hapmap]
rs2687139	0.83[JPT][hapmap]
rs2687140	0.83[JPT][hapmap]
rs2687142	0.83[JPT][hapmap]
rs2687144	0.84[JPT][hapmap]
rs2687145	0.84[JPT][hapmap]
rs2740561	0.87[JPT][hapmap]
rs2740565	0.84[JPT][hapmap]
rs28457808	0.83[ASN][1000 genomes]
rs3137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34777615	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3735453	0.84[JPT][hapmap]
rs3779354	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs3800960	0.85[CHB][hapmap];0.87[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs3801288	0.92[CEU][hapmap];0.81[MEX][hapmap]
rs3843540	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3901286	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs45540134	0.81[ASN][1000 genomes]
rs4646450	0.82[ASW][hapmap];0.85[CEU][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes]
rs4646457	0.83[JPT][hapmap]
rs4729532	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs60301933	0.82[ASN][1000 genomes]
rs61402640	0.84[ASN][1000 genomes]
rs61543997	0.84[ASN][1000 genomes]
rs6465750	0.84[JPT][hapmap]
rs6943920	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs6955490	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs6961634	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6962772	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72494451	0.80[ASN][1000 genomes]
rs72494452	0.80[ASN][1000 genomes]
rs776746	0.84[JPT][hapmap]
rs7794682	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7794705	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7804551	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7808022	0.83[JPT][hapmap]
rs868564	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs883403	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs917154	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs940336	0.85[CHB][hapmap];0.83[JPT][hapmap]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10238965	CYP3A5	cis	parietal	SCAN
rs10238965	CPSF4	cis	parietal	SCAN
rs10238965	ACTL6B	cis	cerebellum	SCAN
rs10238965	GATS	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99132600-99148600	Weak transcription	Brain Angular Gyrus	brain
2	chr7:99138200-99146400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr7:99138600-99148800	Weak transcription	Brain Substantia Nigra	brain
4	chr7:99140000-99148600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr7:99141600-99148400	Weak transcription	Colonic Mucosa	Colon
6	chr7:99141600-99148600	Weak transcription	NHEK	skin
7	chr7:99141800-99148200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr7:99141800-99148200	Weak transcription	Pancreas	Pancrea
9	chr7:99142000-99148800	Weak transcription	Esophagus	oesophagus
10	chr7:99142400-99146000	Strong transcription	Brain Germinal Matrix	brain
11	chr7:99142400-99148200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr7:99142600-99148200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:99143200-99146800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr7:99143400-99146400	Strong transcription	Fetal Brain Female	brain
15	chr7:99143600-99146400	ZNF genes & repeats	Fetal Muscle Leg	muscle
16	chr7:99143600-99146400	Strong transcription	Placenta	Placenta
17	chr7:99143600-99148600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr7:99143600-99148800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr7:99144000-99146000	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr7:99144000-99146200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr7:99144000-99146400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr7:99144000-99146400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr7:99144000-99146400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
24	chr7:99144000-99146600	ZNF genes & repeats	Liver	Liver
25	chr7:99144000-99147000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr7:99144000-99147200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr7:99144200-99146000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr7:99144200-99146200	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr7:99144200-99146200	Strong transcription	Brain Anterior Caudate	brain
30	chr7:99144200-99146200	Strong transcription	HSMM	muscle
31	chr7:99144200-99146400	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr7:99144200-99147000	ZNF genes & repeats	Fetal Lung	lung
33	chr7:99144200-99148600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr7:99144200-99149000	Weak transcription	Aorta	Aorta
35	chr7:99144400-99146200	Strong transcription	Dnd41	blood
36	chr7:99144400-99147200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:99144400-99148200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr7:99144400-99148800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr7:99144400-99148800	Weak transcription	Small Intestine	intestine
40	chr7:99144600-99148200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr7:99144600-99148600	Weak transcription	HUVEC	blood vessel
42	chr7:99144600-99148800	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr7:99144800-99146000	Strong transcription	NHDF-Ad	bronchial
44	chr7:99144800-99146200	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr7:99144800-99146200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr7:99144800-99146200	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr7:99144800-99146200	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr7:99144800-99146200	Strong transcription	Brain Hippocampus Middle	brain
49	chr7:99144800-99146200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
50	chr7:99144800-99146200	ZNF genes & repeats	Fetal Kidney	kidney

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