Variant report

Variant	rs9496944
Chromosome Location	chr6:144677481-144677482
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 130 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs12660406	1.00[EUR][1000 genomes]
rs12660513	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs12660531	1.00[EUR][1000 genomes]
rs12660596	1.00[EUR][1000 genomes]
rs12661781	1.00[EUR][1000 genomes]
rs12661969	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12662267	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12662696	1.00[EUR][1000 genomes]
rs12662724	1.00[EUR][1000 genomes]
rs12662786	1.00[EUR][1000 genomes]
rs12662872	1.00[EUR][1000 genomes]
rs12662904	1.00[EUR][1000 genomes]
rs12663172	1.00[EUR][1000 genomes]
rs12663380	0.84[CHB][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12663605	1.00[EUR][1000 genomes]
rs12663851	1.00[EUR][1000 genomes]
rs12664200	1.00[EUR][1000 genomes]
rs12664245	1.00[EUR][1000 genomes]
rs12664298	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs12664304	1.00[EUR][1000 genomes]
rs12665589	1.00[EUR][1000 genomes]
rs12665850	0.84[CHB][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17073463	1.00[EUR][1000 genomes]
rs17073482	1.00[EUR][1000 genomes]
rs17073498	1.00[EUR][1000 genomes]
rs17073506	1.00[EUR][1000 genomes]
rs17073524	1.00[EUR][1000 genomes]
rs17073528	1.00[EUR][1000 genomes]
rs17073529	1.00[EUR][1000 genomes]
rs17073544	1.00[EUR][1000 genomes]
rs17073571	1.00[EUR][1000 genomes]
rs17073580	1.00[EUR][1000 genomes]
rs17073598	1.00[EUR][1000 genomes]
rs17073602	1.00[EUR][1000 genomes]
rs17073610	1.00[EUR][1000 genomes]
rs17073623	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs17073629	1.00[EUR][1000 genomes]
rs17073631	1.00[EUR][1000 genomes]
rs17073672	0.84[CHB][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17073678	1.00[EUR][1000 genomes]
rs17840301	1.00[EUR][1000 genomes]
rs1998367	1.00[EUR][1000 genomes]
rs34140249	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34502493	1.00[EUR][1000 genomes]
rs35325795	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36007040	1.00[EUR][1000 genomes]
rs3811097	1.00[EUR][1000 genomes]
rs4301321	1.00[EUR][1000 genomes]
rs4896714	1.00[EUR][1000 genomes]
rs4896715	1.00[EUR][1000 genomes]
rs4896717	1.00[EUR][1000 genomes]
rs55684976	1.00[EUR][1000 genomes]
rs56820385	1.00[EUR][1000 genomes]
rs57069580	1.00[EUR][1000 genomes]
rs57380483	1.00[EUR][1000 genomes]
rs57485302	1.00[EUR][1000 genomes]
rs57592921	1.00[EUR][1000 genomes]
rs57679521	1.00[EUR][1000 genomes]
rs57704478	1.00[EUR][1000 genomes]
rs57712072	1.00[EUR][1000 genomes]
rs57751197	1.00[EUR][1000 genomes]
rs58396690	1.00[EUR][1000 genomes]
rs58590469	1.00[EUR][1000 genomes]
rs58646546	0.87[ASN][1000 genomes]
rs58847604	1.00[EUR][1000 genomes]
rs58849686	1.00[EUR][1000 genomes]
rs58857193	1.00[EUR][1000 genomes]
rs59003501	1.00[EUR][1000 genomes]
rs59612420	1.00[EUR][1000 genomes]
rs59614628	1.00[EUR][1000 genomes]
rs59718967	1.00[EUR][1000 genomes]
rs59803839	1.00[EUR][1000 genomes]
rs59810504	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59892317	1.00[ASN][1000 genomes]
rs59936141	1.00[EUR][1000 genomes]
rs60053855	1.00[EUR][1000 genomes]
rs60188478	1.00[EUR][1000 genomes]
rs60234245	1.00[EUR][1000 genomes]
rs60345197	1.00[EUR][1000 genomes]
rs60439721	1.00[EUR][1000 genomes]
rs60484357	1.00[EUR][1000 genomes]
rs60559108	1.00[EUR][1000 genomes]
rs60634096	1.00[EUR][1000 genomes]
rs60811448	1.00[EUR][1000 genomes]
rs60857439	1.00[EUR][1000 genomes]
rs60859726	1.00[EUR][1000 genomes]
rs61087655	1.00[EUR][1000 genomes]
rs61211447	1.00[EUR][1000 genomes]
rs61327932	1.00[EUR][1000 genomes]
rs6570619	0.81[AMR][1000 genomes]
rs6911171	0.83[AMR][1000 genomes]
rs6914753	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6915621	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6916795	1.00[MEX][hapmap];0.95[AMR][1000 genomes]
rs6917261	0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6919115	0.83[AMR][1000 genomes]
rs6922109	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6922608	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6924797	0.95[AMR][1000 genomes]
rs6927798	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs6941296	0.83[AMR][1000 genomes]
rs73588920	0.83[AMR][1000 genomes]
rs73589002	1.00[EUR][1000 genomes]
rs73591113	1.00[EUR][1000 genomes]
rs73594934	1.00[EUR][1000 genomes]
rs73780508	1.00[EUR][1000 genomes]
rs73780540	1.00[EUR][1000 genomes]
rs7741466	1.00[EUR][1000 genomes]
rs7745998	1.00[MEX][hapmap];0.95[AMR][1000 genomes]
rs7747486	1.00[EUR][1000 genomes]
rs7751351	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7751876	1.00[EUR][1000 genomes]
rs7766883	1.00[EUR][1000 genomes]
rs7768531	1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7774175	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321968	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs9321969	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs9484874	1.00[EUR][1000 genomes]
rs9496925	0.83[AMR][1000 genomes]
rs9496928	0.83[AMR][1000 genomes]
rs9496930	0.95[AMR][1000 genomes]
rs9496932	1.00[EUR][1000 genomes]
rs9496935	0.84[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9496938	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9496948	0.81[ASW][hapmap]
rs9496955	1.00[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	nsv830832	chr6:144572378-144759023	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2422260	chr6:144574591-144731630	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144653200-144684600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:144663200-144685800	Weak transcription	Brain Substantia Nigra	brain
3	chr6:144665400-144696400	Weak transcription	Fetal Intestine Small	intestine
4	chr6:144668800-144681600	Weak transcription	Small Intestine	intestine
5	chr6:144670800-144691200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:144671000-144681600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:144671000-144683200	Weak transcription	Gastric	stomach
8	chr6:144671200-144692000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:144671400-144681600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:144671400-144681600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:144671800-144681600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:144671800-144683200	Weak transcription	HSMM	muscle
13	chr6:144671800-144685200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:144672000-144683200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:144673000-144681400	Weak transcription	Esophagus	oesophagus
16	chr6:144673200-144677800	Weak transcription	Pancreas	Pancrea
17	chr6:144673200-144678400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:144673200-144679800	Weak transcription	Ovary	ovary
19	chr6:144673200-144681400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:144673200-144683000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr6:144673200-144683200	Weak transcription	Liver	Liver
22	chr6:144673200-144683200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:144673400-144678800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr6:144673400-144678800	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr6:144673400-144681400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:144673400-144681400	Weak transcription	NHEK	skin
27	chr6:144673400-144681600	Weak transcription	Right Atrium	heart
28	chr6:144673400-144683200	Weak transcription	Stomach Mucosa	stomach
29	chr6:144673400-144683400	Weak transcription	Colon Smooth Muscle	Colon
30	chr6:144673400-144699600	Weak transcription	Fetal Stomach	stomach
31	chr6:144673800-144678000	Enhancers	Primary T cells from cord blood	blood
32	chr6:144673800-144681600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:144673800-144682800	Weak transcription	Fetal Muscle Leg	muscle
34	chr6:144674200-144680200	Weak transcription	HUVEC	blood vessel
35	chr6:144674200-144680600	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr6:144674200-144681600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr6:144674200-144683400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr6:144675400-144680200	Weak transcription	Fetal Heart	heart
39	chr6:144675400-144681400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr6:144675400-144685600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr6:144675600-144681600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr6:144675600-144692000	Weak transcription	Dnd41	blood
43	chr6:144675800-144678200	Weak transcription	Lung	lung
44	chr6:144675800-144679000	Weak transcription	Adipose Nuclei	Adipose
45	chr6:144675800-144680200	Weak transcription	Aorta	Aorta
46	chr6:144675800-144680200	Weak transcription	Psoas Muscle	Psoas
47	chr6:144675800-144681600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:144675800-144681600	Weak transcription	HepG2	liver
49	chr6:144675800-144684000	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr6:144675800-144687000	Enhancers	Primary T helper cells PMA-I stimulated	--

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