Variant report

Variant	rs10844656
Chromosome Location	chr12:9893079-9893080
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	chr12:9884042..9890048-chr12:9890384..9897967,9	K562	blood:
2	chr12:9889267..9893240-chr12:9909352..9912451,4	K562	blood:

Variant related genes	Relation type
ENSG00000184293	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10161013	0.94[EUR][1000 genomes]
rs10492164	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs10743828	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10772093	0.92[CEU][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes]
rs10772099	0.95[EUR][1000 genomes]
rs1134543	0.82[EUR][1000 genomes]
rs11835594	0.85[CEU][hapmap];0.94[EUR][1000 genomes]
rs12304982	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs12820281	0.95[EUR][1000 genomes]
rs12824727	0.93[EUR][1000 genomes]
rs13377908	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs13377939	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs16923367	0.92[CEU][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs16927874	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs17806015	0.83[GIH][hapmap]
rs2080210	0.81[EUR][1000 genomes]
rs2268145	0.94[EUR][1000 genomes]
rs2401387	0.82[EUR][1000 genomes]
rs2401388	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs3136576	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3176793	1.00[CHD][hapmap]
rs34584384	0.89[EUR][1000 genomes]
rs34633868	0.91[EUR][1000 genomes]
rs35990903	0.94[EUR][1000 genomes]
rs3922289	0.93[EUR][1000 genomes]
rs4611290	0.82[EUR][1000 genomes]
rs4763296	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4763864	0.91[EUR][1000 genomes]
rs55715780	0.82[EUR][1000 genomes]
rs56980650	0.82[EUR][1000 genomes]
rs59016059	0.94[EUR][1000 genomes]
rs59210706	0.82[EUR][1000 genomes]
rs6488120	0.80[EUR][1000 genomes]
rs6488121	0.80[EUR][1000 genomes]
rs6488123	0.92[CEU][hapmap];0.86[MEX][hapmap];0.80[EUR][1000 genomes]
rs6488176	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71447599	0.95[EUR][1000 genomes]
rs71447600	0.94[EUR][1000 genomes]
rs7301386	0.94[EUR][1000 genomes]
rs74062704	0.82[EUR][1000 genomes]
rs74062708	0.85[EUR][1000 genomes]
rs74065337	0.82[EUR][1000 genomes]
rs74065339	0.82[EUR][1000 genomes]
rs74065340	0.82[EUR][1000 genomes]
rs7962964	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs7964917	0.94[EUR][1000 genomes]
rs7967436	0.80[EUR][1000 genomes]
rs7969022	1.00[CEU][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7976474	0.92[CEU][hapmap];0.94[EUR][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	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv983235	chr12:9852218-9893776	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10844656	RP11-75L1.2	cis	Nerve Tibial	GTEx
rs10844656	C12orf53	cis	parietal	SCAN
rs10844656	RP11-75L1.2	cis	Skin Sun Exposed Lower leg	GTEx
rs10844656	SPSB2	cis	cerebellum	SCAN
rs10844656	RP11-75L1.2	cis	Adipose Subcutaneous	GTEx
rs10844656	RP11-75L1.2	cis	lung	GTEx
rs10844656	RP11-75L1.2	cis	Whole Blood	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9886000-9894600	Enhancers	Primary B cells from cord blood	blood
2	chr12:9887600-9893800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:9889000-9895200	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr12:9890400-9893800	Weak transcription	Dnd41	blood
5	chr12:9890400-9895200	Weak transcription	Hela-S3	cervix
6	chr12:9890400-9897600	Weak transcription	HUVEC	blood vessel
7	chr12:9892000-9893200	Active TSS	Pancreas	Pancrea
8	chr12:9892000-9893400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:9892400-9894800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:9892400-9895800	Enhancers	Primary hematopoietic stem cells	blood
11	chr12:9892600-9893600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:9892600-9894800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr12:9892600-9894800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:9892800-9893200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr12:9892800-9893200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
16	chr12:9892800-9893200	Enhancers	Esophagus	oesophagus
17	chr12:9892800-9893200	Flanking Active TSS	GM12878-XiMat	blood
18	chr12:9892800-9893400	Enhancers	Adipose Nuclei	Adipose
19	chr12:9892800-9893600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr12:9892800-9893600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr12:9892800-9893800	Enhancers	Fetal Thymus	thymus
22	chr12:9892800-9894400	Enhancers	Primary T cells from cord blood	blood
23	chr12:9892800-9894400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr12:9892800-9894600	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr12:9892800-9895200	Weak transcription	Colonic Mucosa	Colon
26	chr12:9892800-9895200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr12:9892800-9903200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:9893000-9893200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:9893000-9893200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:9893000-9893200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr12:9893000-9893200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr12:9893000-9893200	Enhancers	Placenta	Placenta
33	chr12:9893000-9893200	Enhancers	Left Ventricle	heart
34	chr12:9893000-9893400	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr12:9893000-9893400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr12:9893000-9893400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:9893000-9893400	Enhancers	Lung	lung
38	chr12:9893000-9893400	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr12:9893000-9893400	Enhancers	Stomach Mucosa	stomach
40	chr12:9893000-9893600	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr12:9893000-9893600	Enhancers	Primary T cells fromperipheralblood	blood
42	chr12:9893000-9893600	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr12:9893000-9893600	Flanking Active TSS	K562	blood
44	chr12:9893000-9894200	Weak transcription	Thymus	Thymus
45	chr12:9893000-9894800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr12:9893000-9895200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:9893000-9895400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr12:9893000-9896400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:9893000-9896800	Enhancers	Primary B cells from peripheral blood	blood

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