Variant report

Variant	rs3748236
Chromosome Location	chr10:98369536-98369537
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:98366804..98369956-chr10:98370785..98374405,6	K562	blood:
2	chr10:98367008..98370019-chr10:98371148..98375452,4	K562	blood:

Extended variants
information (count: 120 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs1018604	0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs1018605	0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs1051450	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1063605	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10736114	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs10882809	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10882811	0.83[JPT][hapmap]
rs10882813	0.83[JPT][hapmap]
rs10882815	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10882821	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10882826	0.82[ASN][1000 genomes]
rs10882827	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10882828	0.83[ASN][1000 genomes]
rs11188809	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11188810	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11188811	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11188813	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11188814	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11188815	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11188817	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11188821	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11188822	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11188825	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11188831	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11188832	0.88[ASN][1000 genomes]
rs11188833	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11188840	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11188842	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11188844	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11188847	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11188848	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11188853	0.94[ASN][1000 genomes]
rs11188854	0.82[ASN][1000 genomes]
rs11188856	0.83[JPT][hapmap]
rs11188858	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1132913	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1132914	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1156035	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1156036	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11814010	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12218847	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12219275	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs12220047	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12221143	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12221262	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12414612	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12415048	0.82[ASN][1000 genomes]
rs12416646	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12761817	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12766248	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12775533	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12776810	0.91[ASN][1000 genomes]
rs12779720	0.83[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12784975	0.89[MEX][hapmap];0.80[AMR][1000 genomes]
rs1324255	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1324256	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1324259	0.85[ASN][1000 genomes]
rs1324261	0.92[ASN][1000 genomes]
rs1408367	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17391547	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17482382	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1983831	0.82[ASN][1000 genomes]
rs2011190	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2025451	0.85[ASN][1000 genomes]
rs2031326	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs33964467	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs35779764	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs36098523	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3689	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3748234	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs3748235	0.80[ASN][1000 genomes]
rs3748237	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3748238	0.80[AMR][1000 genomes]
rs3789957	0.83[JPT][hapmap]
rs3789958	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3818389	0.83[JPT][hapmap]
rs41317270	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4146727	1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs4485036	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4534508	0.94[CEU][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.82[ASN][1000 genomes]
rs4917742	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs4919029	0.83[JPT][hapmap]
rs4919032	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4919037	0.85[ASN][1000 genomes]
rs4919040	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs58305369	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61858194	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61858494	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61859300	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7069429	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs7070686	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7071044	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7071224	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7071881	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7073017	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7073682	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7074516	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7082873	0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7085389	0.91[ASN][1000 genomes]
rs7086213	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7086240	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7087478	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7091606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7097291	0.85[ASN][1000 genomes]
rs7101320	0.89[ASN][1000 genomes]
rs713251	0.88[CEU][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs727329	0.82[ASN][1000 genomes]
rs7448	0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs7478356	0.82[ASN][1000 genomes]
rs7914154	0.83[JPT][hapmap]
rs7919739	0.83[JPT][hapmap]
rs8578	0.80[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs912480	0.83[JPT][hapmap]
rs927639	0.89[ASN][1000 genomes]
rs9633703	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs9664749	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9664955	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413353	chr10:98039370-98561524	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv895909	chr10:98354924-98382165	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3748236	FRA10AC1	cis	parietal	SCAN
rs3748236	CWF19L1	cis	cerebellum	SCAN
rs3748236	SCD	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98348000-98373600	Weak transcription	Left Ventricle	heart
2	chr10:98350800-98395600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr10:98352400-98378600	Strong transcription	Liver	Liver
4	chr10:98352400-98399400	Strong transcription	Primary B cells from peripheral blood	blood
5	chr10:98352600-98403000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr10:98353000-98388400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr10:98353000-98403000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr10:98354600-98388600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr10:98354800-98370600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr10:98357800-98382000	Strong transcription	GM12878-XiMat	blood
11	chr10:98358600-98370400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr10:98358800-98369600	Weak transcription	Gastric	stomach
13	chr10:98359400-98373400	Weak transcription	Right Ventricle	heart
14	chr10:98360400-98392800	Weak transcription	Thymus	Thymus
15	chr10:98362200-98389200	Strong transcription	Primary B cells from cord blood	blood
16	chr10:98362600-98373600	Weak transcription	Lung	lung
17	chr10:98363800-98392600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr10:98365600-98374200	Enhancers	Fetal Intestine Large	intestine
19	chr10:98365600-98374400	Enhancers	Fetal Intestine Small	intestine
20	chr10:98365800-98369800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr10:98365800-98370000	Enhancers	Ovary	ovary
22	chr10:98366000-98370600	Strong transcription	Spleen	Spleen
23	chr10:98366000-98388400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr10:98366200-98370400	Strong transcription	Primary hematopoietic stem cells	blood
25	chr10:98366400-98373400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr10:98366600-98392600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr10:98367200-98372800	Strong transcription	Pancreas	Pancrea
28	chr10:98367200-98375000	Enhancers	Stomach Mucosa	stomach
29	chr10:98367200-98376200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr10:98367400-98370400	Enhancers	Duodenum Mucosa	Duodenum
31	chr10:98367400-98375000	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr10:98367400-98376200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr10:98367400-98418600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr10:98367600-98372000	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr10:98367800-98371800	Enhancers	Colonic Mucosa	Colon
36	chr10:98368400-98373600	Weak transcription	HSMM	muscle
37	chr10:98368600-98370200	Strong transcription	Placenta	Placenta
38	chr10:98368600-98371800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr10:98368800-98377800	Weak transcription	Brain Anterior Caudate	brain
40	chr10:98369000-98373400	Weak transcription	HSMMtube	muscle
41	chr10:98369200-98372600	Enhancers	HepG2	liver
42	chr10:98369400-98370600	Enhancers	Small Intestine	intestine
43	chr10:98369400-98371000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr10:98369400-98371000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr10:98369400-98371000	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr10:98369400-98371200	Enhancers	Primary T cells fromperipheralblood	blood

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