Variant report

Variant	rs12241564
Chromosome Location	chr10:98725915-98725916
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10437452	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188929	1.00[ASN][1000 genomes]
rs11188937	1.00[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs11188939	1.00[GIH][hapmap]
rs11188940	0.81[EUR][1000 genomes]
rs11188947	0.81[EUR][1000 genomes]
rs11188954	0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs11188955	0.87[EUR][1000 genomes]
rs11188956	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs11188959	1.00[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs11188967	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11188971	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11188978	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188999	1.00[ASN][1000 genomes]
rs12240946	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12241405	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12242141	0.85[LWK][hapmap];0.86[YRI][hapmap]
rs12242330	1.00[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs12243551	1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs12244490	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12246067	0.81[EUR][1000 genomes]
rs12247344	0.84[EUR][1000 genomes]
rs12248349	1.00[ASN][1000 genomes]
rs12249381	1.00[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs12249427	0.87[EUR][1000 genomes]
rs12249891	0.81[EUR][1000 genomes]
rs12250548	1.00[ASN][1000 genomes]
rs12252424	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12252435	0.81[EUR][1000 genomes]
rs12254525	0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs12256424	0.81[EUR][1000 genomes]
rs12257413	0.87[EUR][1000 genomes]
rs12258355	0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs12258469	0.87[EUR][1000 genomes]
rs12259265	0.81[EUR][1000 genomes]
rs12261278	0.81[EUR][1000 genomes]
rs12261881	0.81[EUR][1000 genomes]
rs12262784	1.00[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs12263331	0.87[EUR][1000 genomes]
rs12264014	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12264950	1.00[ASN][1000 genomes]
rs12265242	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs12265606	1.00[ASN][1000 genomes]
rs12266068	0.81[EUR][1000 genomes]
rs12266185	0.81[EUR][1000 genomes]
rs12267926	0.81[EUR][1000 genomes]
rs12268216	0.85[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs12268272	1.00[CEU][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs13376965	0.87[EUR][1000 genomes]
rs17112175	1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs17112190	1.00[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs2104785	0.81[EUR][1000 genomes]
rs2183449	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28439735	0.87[EUR][1000 genomes]
rs28505353	1.00[ASN][1000 genomes]
rs28758432	0.87[EUR][1000 genomes]
rs4394767	0.89[EUR][1000 genomes]
rs55855950	1.00[ASN][1000 genomes]
rs56327223	1.00[ASN][1000 genomes]
rs56867696	0.87[EUR][1000 genomes]
rs57501540	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57716318	0.81[EUR][1000 genomes]
rs58270704	1.00[ASN][1000 genomes]
rs58376960	0.86[EUR][1000 genomes]
rs58409956	1.00[ASN][1000 genomes]
rs59938221	0.84[EUR][1000 genomes]
rs59999388	0.87[EUR][1000 genomes]
rs60576681	0.87[EUR][1000 genomes]
rs61492214	0.87[EUR][1000 genomes]
rs6584101	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071211	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7072273	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs7073150	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7081197	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082316	0.87[EUR][1000 genomes]
rs7082838	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085822	1.00[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs7085851	0.87[EUR][1000 genomes]
rs7086875	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7090441	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7090690	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7090880	1.00[ASN][1000 genomes]
rs72821721	1.00[ASN][1000 genomes]
rs72821744	1.00[ASN][1000 genomes]
rs72821759	1.00[ASN][1000 genomes]
rs73318637	1.00[ASN][1000 genomes]
rs73318641	1.00[ASN][1000 genomes]
rs73320607	1.00[ASN][1000 genomes]
rs74153734	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7893325	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7894138	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7894418	0.81[EUR][1000 genomes]
rs7895914	1.00[ASN][1000 genomes]
rs7906294	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910221	0.86[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs7918085	1.00[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs7920238	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921193	0.81[EUR][1000 genomes]
rs7921216	0.81[EUR][1000 genomes]
rs7921885	1.00[GIH][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1052931	chr10:98676192-98862301	Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1042398	chr10:98691406-98851346	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv831951	chr10:98717103-98761280	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12241564	CRTAC1	cis	parietal	SCAN
rs12241564	CCNJ	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98709200-98736200	Weak transcription	Psoas Muscle	Psoas
2	chr10:98712800-98731200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:98715400-98726400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr10:98715400-98733800	Weak transcription	A549	lung
5	chr10:98715400-98740600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr10:98715400-98740600	Weak transcription	Aorta	Aorta
7	chr10:98715400-98740600	Weak transcription	Esophagus	oesophagus
8	chr10:98715600-98731000	Weak transcription	Small Intestine	intestine
9	chr10:98715600-98735600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr10:98715600-98740600	Weak transcription	Fetal Stomach	stomach
11	chr10:98715600-98740600	Weak transcription	NHEK	skin
12	chr10:98715800-98740600	Weak transcription	Lung	lung
13	chr10:98716000-98732200	Weak transcription	GM12878-XiMat	blood
14	chr10:98716000-98733600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr10:98716000-98737600	Weak transcription	Thymus	Thymus
16	chr10:98716000-98740200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr10:98716000-98740400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr10:98716000-98740600	Weak transcription	Brain Anterior Caudate	brain
19	chr10:98716000-98740600	Weak transcription	Gastric	stomach
20	chr10:98716000-98740600	Weak transcription	Left Ventricle	heart
21	chr10:98716000-98740600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr10:98716000-98741000	Weak transcription	Brain Germinal Matrix	brain
23	chr10:98716200-98740800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr10:98716400-98726000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr10:98716400-98740600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr10:98716600-98739800	Weak transcription	Primary T cells from cord blood	blood
27	chr10:98716600-98740600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr10:98716600-98740600	Weak transcription	Ovary	ovary
29	chr10:98716600-98740600	Weak transcription	HMEC	breast
30	chr10:98716600-98743200	Weak transcription	Hela-S3	cervix
31	chr10:98716800-98727400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr10:98716800-98733400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr10:98716800-98740600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr10:98717000-98740600	Weak transcription	Fetal Kidney	kidney
35	chr10:98717200-98728200	Weak transcription	Liver	Liver
36	chr10:98717400-98726200	Weak transcription	Fetal Intestine Small	intestine
37	chr10:98717400-98740600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr10:98717800-98740600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr10:98718200-98733800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr10:98718600-98740400	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr10:98718600-98740600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr10:98719000-98740600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr10:98719000-98740600	Weak transcription	Dnd41	blood
44	chr10:98719200-98732000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr10:98719200-98733600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr10:98719800-98740600	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr10:98720000-98739200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr10:98720000-98740400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr10:98720000-98740600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr10:98720000-98740600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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