Variant report

Variant	rs12664200
Chromosome Location	chr6:144744844-144744845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs12660406	1.00[EUR][1000 genomes]
rs12660513	1.00[EUR][1000 genomes]
rs12660531	1.00[EUR][1000 genomes]
rs12660596	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12661781	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12661969	1.00[EUR][1000 genomes]
rs12662267	1.00[EUR][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	1.00[EUR][1000 genomes]
rs12663605	1.00[EUR][1000 genomes]
rs12663851	1.00[EUR][1000 genomes]
rs12664245	1.00[EUR][1000 genomes]
rs12664298	1.00[EUR][1000 genomes]
rs12664304	1.00[EUR][1000 genomes]
rs12665589	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12665850	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[EUR][1000 genomes]
rs17073629	1.00[EUR][1000 genomes]
rs17073631	1.00[EUR][1000 genomes]
rs17073672	1.00[EUR][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]
rs35325795	1.00[EUR][1000 genomes]
rs36007040	1.00[EUR][1000 genomes]
rs3811097	1.00[EUR][1000 genomes]
rs3811098	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs4301321	1.00[EUR][1000 genomes]
rs4896714	0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4896715	0.90[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4896717	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55684976	1.00[EUR][1000 genomes]
rs56820385	1.00[EUR][1000 genomes]
rs57380483	1.00[EUR][1000 genomes]
rs57485302	1.00[EUR][1000 genomes]
rs57679521	1.00[EUR][1000 genomes]
rs57704478	1.00[EUR][1000 genomes]
rs58396690	1.00[EUR][1000 genomes]
rs58590469	1.00[EUR][1000 genomes]
rs58849686	1.00[EUR][1000 genomes]
rs58857193	1.00[EUR][1000 genomes]
rs59003501	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]
rs59936141	1.00[EUR][1000 genomes]
rs60053855	1.00[EUR][1000 genomes]
rs60234245	1.00[EUR][1000 genomes]
rs60345197	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60439721	1.00[EUR][1000 genomes]
rs60484357	1.00[EUR][1000 genomes]
rs60559108	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]
rs6570627	1.00[GIH][hapmap]
rs6914753	1.00[EUR][1000 genomes]
rs6915621	1.00[EUR][1000 genomes]
rs6917261	1.00[EUR][1000 genomes]
rs6922109	1.00[EUR][1000 genomes]
rs6922608	1.00[EUR][1000 genomes]
rs6923287	1.00[YRI][hapmap]
rs6927798	1.00[EUR][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]
rs7738289	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7741466	1.00[EUR][1000 genomes]
rs7747486	1.00[EUR][1000 genomes]
rs7751351	1.00[EUR][1000 genomes]
rs7757257	1.00[YRI][hapmap]
rs7766883	1.00[EUR][1000 genomes]
rs7768531	1.00[EUR][1000 genomes]
rs7773862	0.99[ASN][1000 genomes]
rs7774175	1.00[EUR][1000 genomes]
rs7774376	1.00[CHB][hapmap];0.99[ASN][1000 genomes]
rs7776211	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9484874	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9484875	0.99[ASN][1000 genomes]
rs9496932	1.00[EUR][1000 genomes]
rs9496935	1.00[EUR][1000 genomes]
rs9496938	1.00[EUR][1000 genomes]
rs9496944	1.00[EUR][1000 genomes]
rs9496955	1.00[EUR][1000 genomes]
rs9496962	0.99[ASN][1000 genomes]
rs9496963	0.97[ASN][1000 genomes]
rs9496964	1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	nsv1023014	chr6:144717963-144806691	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv886739	chr6:144719765-144796516	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144720000-144758200	Weak transcription	Fetal Intestine Small	intestine
2	chr6:144726800-144745200	Weak transcription	Fetal Stomach	stomach
3	chr6:144729800-144761400	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:144733200-144756800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:144737000-144752200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr6:144737800-144747400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:144737800-144755400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:144737800-144756800	Weak transcription	Right Ventricle	heart
9	chr6:144738000-144745200	Weak transcription	HSMM	muscle
10	chr6:144738000-144751000	Weak transcription	NH-A	brain
11	chr6:144738000-144753000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:144738000-144755400	Weak transcription	HMEC	breast
13	chr6:144738000-144755400	Weak transcription	NHEK	skin
14	chr6:144738400-144757000	Weak transcription	Fetal Heart	heart
15	chr6:144738600-144750600	Weak transcription	Psoas Muscle	Psoas
16	chr6:144739000-144756800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr6:144739200-144747400	Weak transcription	NHLF	lung
18	chr6:144739200-144755400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:144739200-144755600	Weak transcription	Small Intestine	intestine
20	chr6:144739200-144755600	Weak transcription	A549	lung
21	chr6:144740600-144758800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:144740800-144761200	Weak transcription	Brain Hippocampus Middle	brain
23	chr6:144740800-144761400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:144740800-144787600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:144741000-144756800	Weak transcription	Right Atrium	heart
26	chr6:144741000-144801800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr6:144741200-144747200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:144741200-144760800	Weak transcription	Fetal Brain Male	brain
29	chr6:144742000-144747400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:144742800-144745600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:144742800-144753600	Strong transcription	Primary T cells from cord blood	blood
32	chr6:144742800-144753800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr6:144742800-144761200	Weak transcription	Colonic Mucosa	Colon
34	chr6:144743000-144747800	Strong transcription	Liver	Liver
35	chr6:144743000-144748000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr6:144743000-144749400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
37	chr6:144743000-144751400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr6:144743000-144753600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr6:144743000-144753600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr6:144743000-144753800	Strong transcription	Primary B cells from cord blood	blood
41	chr6:144743000-144753800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr6:144743000-144753800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:144743000-144753800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:144743000-144753800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:144743000-144753800	Strong transcription	Fetal Thymus	thymus
46	chr6:144743000-144753800	Strong transcription	Dnd41	blood
47	chr6:144743000-144753800	Strong transcription	GM12878-XiMat	blood
48	chr6:144743000-144753800	Strong transcription	HepG2	liver
49	chr6:144743000-144753800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr6:144743000-144780200	Strong transcription	Primary T cells fromperipheralblood	blood

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