Variant report

Variant	rs12664849
Chromosome Location	chr6:12139220-12139221
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:12132409..12134498-chr6:12138721..12141080,2	K562	blood:
2	chr6:12132998..12134501-chr6:12138713..12141080,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10947756	0.81[GIH][hapmap]
rs12662314	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12663812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12664121	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs16872348	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2157492	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2157494	0.86[MEX][hapmap]
rs2228211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2327512	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28769650	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777756	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3777757	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777767	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777772	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777777	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800499	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4317394	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4443504	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484521	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4714187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55637995	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6910367	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6917623	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931770	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72828103	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72828104	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72828110	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7449638	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7741589	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7747677	0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs9380769	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830586	chr6:12130076-12295334	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12664849	JARID2	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12121400-12150200	Weak transcription	Fetal Brain Male	brain
2	chr6:12122200-12161800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:12122400-12139800	Weak transcription	Esophagus	oesophagus
4	chr6:12122800-12139400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:12122800-12142800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:12124400-12139600	Weak transcription	Fetal Brain Female	brain
7	chr6:12128600-12148400	Weak transcription	Fetal Heart	heart
8	chr6:12130800-12139400	Weak transcription	Psoas Muscle	Psoas
9	chr6:12134800-12149600	Weak transcription	Brain Angular Gyrus	brain
10	chr6:12135000-12140200	Weak transcription	Aorta	Aorta
11	chr6:12136200-12139600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr6:12136800-12139400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:12137000-12163600	Weak transcription	Small Intestine	intestine
14	chr6:12137600-12140800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:12137800-12139400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:12137800-12139400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:12137800-12139600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr6:12137800-12140800	Strong transcription	Liver	Liver
19	chr6:12137800-12141000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
20	chr6:12137800-12141000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
21	chr6:12138000-12139400	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr6:12138000-12139600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr6:12138200-12139400	Strong transcription	Primary B cells from cord blood	blood
24	chr6:12138200-12139400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
25	chr6:12138200-12139400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:12138200-12139400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr6:12138200-12140200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
28	chr6:12138200-12140600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:12138200-12141000	ZNF genes & repeats	Fetal Intestine Small	intestine
30	chr6:12138200-12141200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:12138200-12141200	Strong transcription	Fetal Lung	lung
32	chr6:12138400-12139800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr6:12138400-12139800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr6:12138400-12141800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr6:12138400-12148000	Weak transcription	Osteobl	bone
36	chr6:12138400-12148400	Weak transcription	Hela-S3	cervix
37	chr6:12138600-12139400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:12138600-12139400	Strong transcription	HSMM	muscle
39	chr6:12138600-12139600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
40	chr6:12138600-12139600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr6:12138600-12139600	ZNF genes & repeats	GM12878-XiMat	blood
42	chr6:12138600-12139600	Strong transcription	NHEK	skin
43	chr6:12138600-12139800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
44	chr6:12138600-12139800	Strong transcription	Primary hematopoietic stem cells	blood
45	chr6:12138600-12140000	Strong transcription	NHDF-Ad	bronchial
46	chr6:12138600-12140200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
47	chr6:12138600-12140200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:12138600-12140200	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr6:12138600-12140400	Strong transcription	Brain Germinal Matrix	brain
50	chr6:12138600-12140400	Strong transcription	Colonic Mucosa	Colon

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