Variant report

Variant	rs12247779
Chromosome Location	chr10:1107957-1107958
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:1090197..1098635-chr10:1098667..1108160,39	K562	blood:
2	chr10:1106369..1108344-chr10:1116985..1118737,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067064	Chromatin interaction
ENSG00000047056	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10047269	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10047382	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10219038	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10794720	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11250242	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11250252	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11250264	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11815047	0.82[ASN][1000 genomes]
rs11818314	1.00[CHB][hapmap]
rs11819178	0.89[ASN][1000 genomes]
rs11819230	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12241632	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs12247818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12268949	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12359250	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13377037	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs17155821	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs17155886	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2279256	0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs2892254	0.87[ASN][1000 genomes]
rs3793776	0.90[CHB][hapmap]
rs3793780	1.00[CHB][hapmap]
rs3793781	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs41299206	0.85[ASN][1000 genomes]
rs57514701	0.80[EUR][1000 genomes]
rs61571350	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7071670	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7093915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7100114	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs74117831	0.80[EUR][1000 genomes]
rs74120451	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7922760	0.88[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv540386	chr10:224406-1197416	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1054659	chr10:611444-1133578	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
3	nsv466697	chr10:734229-1129527	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv549765	chr10:734229-1129527	Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv530116	chr10:776548-1401075	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv1052540	chr10:887562-1300134	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv540407	chr10:887562-1300134	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv533861	chr10:945438-1382068	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv530117	chr10:945438-1729634	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
10	nsv540408	chr10:955835-1260680	Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv817532	chr10:964660-1885945	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv1050577	chr10:986723-1277854	Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv540409	chr10:986723-1277854	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
14	nsv949405	chr10:1010464-1376105	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv1048254	chr10:1016006-1146595	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
16	nsv1040178	chr10:1024910-1126104	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
17	nsv540410	chr10:1024910-1126104	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
18	nsv894722	chr10:1058837-1274538	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
19	nsv1046220	chr10:1064024-1188998	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
20	nsv894723	chr10:1073684-1259485	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
21	nsv894724	chr10:1084942-1116294	Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12247779	GTPBP4///IDI2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:1103600-1108200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr10:1103600-1109000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr10:1103600-1109600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr10:1103600-1110400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:1103600-1119400	Weak transcription	Aorta	Aorta
6	chr10:1103600-1119600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr10:1103800-1108600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr10:1103800-1108800	Weak transcription	Fetal Stomach	stomach
9	chr10:1103800-1109400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr10:1103800-1118200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr10:1104000-1109400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr10:1104200-1108000	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr10:1104200-1108200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr10:1104200-1108200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr10:1104200-1108400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr10:1104200-1108600	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr10:1104200-1109000	Weak transcription	Fetal Brain Female	brain
18	chr10:1104200-1109200	Weak transcription	Placenta	Placenta
19	chr10:1104200-1109400	Weak transcription	Brain Substantia Nigra	brain
20	chr10:1104200-1109400	Weak transcription	Colonic Mucosa	Colon
21	chr10:1104200-1116800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr10:1104200-1116800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr10:1104200-1118000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr10:1104200-1118200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr10:1104200-1118200	Weak transcription	Brain Angular Gyrus	brain
26	chr10:1104200-1119200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr10:1104200-1119200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr10:1104200-1119600	Weak transcription	Fetal Lung	lung
29	chr10:1104200-1119600	Weak transcription	Psoas Muscle	Psoas
30	chr10:1104200-1119600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr10:1104400-1108400	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr10:1104400-1109000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr10:1104400-1109200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr10:1104400-1109200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr10:1104400-1109200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr10:1104400-1109200	Weak transcription	NHLF	lung
37	chr10:1104400-1109400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr10:1104400-1109600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr10:1104400-1109600	Weak transcription	Brain Anterior Caudate	brain
40	chr10:1104400-1110800	Weak transcription	Hela-S3	cervix
41	chr10:1104400-1111000	Weak transcription	NHDF-Ad	bronchial
42	chr10:1104400-1112000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr10:1104400-1115800	Weak transcription	Ovary	ovary
44	chr10:1104400-1116800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr10:1104400-1116800	Weak transcription	Small Intestine	intestine
46	chr10:1104400-1118000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr10:1104400-1118000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr10:1104400-1118000	Weak transcription	Fetal Muscle Leg	muscle
49	chr10:1104400-1118000	Weak transcription	HSMMtube	muscle
50	chr10:1104400-1119600	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links