Variant report

Variant	rs1026442
Chromosome Location	chr12:10765031-10765032
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:10764611-10766584	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:10764397-10767179	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:10764557-10765685	Hela-S3	cervix:	n/a	n/a
4	HCFC1	chr12:10765011-10767004	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr12:10764827-10765105	H1-hESC	embryonic stem cell:	n/a	n/a
6	TBL1XR1	chr12:10764900-10765242	K562	blood:	n/a	n/a
7	MYC	chr12:10764936-10765039	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr12:10764756-10765081	K562	blood:	n/a	n/a
9	POLR2A	chr12:10764544-10767138	GM18505	blood:	n/a	n/a
10	POLR2A	chr12:10764672-10765102	HepG2	liver:	n/a	n/a
11	POLR2A	chr12:10764551-10765079	SK-N-MC	brain:	n/a	n/a
12	POLR2A	chr12:10764974-10767096	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr12:10764431-10767480	GM12891	blood:	n/a	n/a
14	POLR2A	chr12:10764541-10767013	IMR90	lung:	n/a	n/a
15	POLR2A	chr12:10764392-10767145	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:10764687-10765035	K562	blood:	n/a	n/a
17	POLR2A	chr12:10759407-10766713	K562	blood:	n/a	n/a
18	POLR2A	chr12:10765003-10765103	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:10754715..10757719-chr12:10762132..10766161,5	MCF-7	breast:
2	chr12:10763668..10768180-chr12:10873034..10877438,4	K562	blood:
3	chr12:10764890..10767963-chr12:10824892..10828037,6	MCF-7	breast:
4	chr12:10757768..10761323-chr12:10763648..10767654,5	MCF-7	breast:
5	chr12:10759828..10762348-chr12:10763400..10769792,9	K562	blood:
6	chr12:10763668..10768484-chr12:10873757..10876876,5	K562	blood:

No data

Variant related genes	Relation type
MAGOHB	TF binding region
ENSG00000060140	Chromatin interaction
ENSG00000060138	Chromatin interaction
ENSG00000111196	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10083164	0.83[JPT][hapmap]
rs10431297	0.82[JPT][hapmap]
rs1054396	0.92[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1073305	0.82[JPT][hapmap]
rs10743911	0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs10772334	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10772340	0.82[JPT][hapmap]
rs10772343	0.81[JPT][hapmap]
rs10772347	0.82[JPT][hapmap]
rs10845180	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10845181	0.82[JPT][hapmap]
rs10845183	0.96[ASN][1000 genomes]
rs10845185	0.83[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs10845192	0.82[JPT][hapmap]
rs10845194	0.81[JPT][hapmap]
rs10845195	0.82[JPT][hapmap]
rs10845197	0.80[JPT][hapmap]
rs10845198	0.82[JPT][hapmap]
rs11053877	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11053880	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11053881	1.00[JPT][hapmap]
rs11053882	1.00[JPT][hapmap]
rs12306757	1.00[JPT][hapmap]
rs12306815	1.00[JPT][hapmap]
rs12811247	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1870194	0.82[GIH][hapmap];1.00[JPT][hapmap]
rs2125091	0.92[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2219382	1.00[JPT][hapmap]
rs2290718	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2305853	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2418087	0.82[JPT][hapmap]
rs2418088	0.82[JPT][hapmap]
rs2900513	0.82[JPT][hapmap]
rs3759264	1.00[JPT][hapmap]
rs3759265	0.93[JPT][hapmap]
rs3782674	1.00[JPT][hapmap]
rs4763565	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6488316	0.82[JPT][hapmap]
rs7312261	1.00[JPT][hapmap]
rs7313620	0.81[JPT][hapmap]
rs7350557	0.82[JPT][hapmap]
rs7350597	0.82[JPT][hapmap]
rs7968284	0.82[JPT][hapmap]
rs7968819	0.89[ASN][1000 genomes]
rs7971142	0.82[JPT][hapmap]
rs897880	1.00[JPT][hapmap]
rs897882	1.00[JPT][hapmap]
rs9988929	0.92[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][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	nsv832329	chr12:10677094-10845946	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1026442	CLEC4E	cis	parietal	SCAN
rs1026442	KLRC3	cis	parietal	SCAN
rs1026442	LRP6	cis	parietal	SCAN
rs1026442	TAS2R43	cis	parietal	SCAN
rs1026442	KLRA1	cis	parietal	SCAN
rs1026442	C1RL	cis	parietal	SCAN
rs1026442	KLRC2	cis	cerebellum	SCAN
rs1026442	KLRA1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10743400-10765400	Weak transcription	Gastric	stomach
2	chr12:10744000-10765200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:10744000-10765400	Weak transcription	Aorta	Aorta
4	chr12:10744200-10765400	Weak transcription	Esophagus	oesophagus
5	chr12:10753600-10765400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:10758000-10765200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:10761400-10765200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:10762400-10765200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:10763000-10765200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:10763000-10765400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:10763800-10765200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr12:10764000-10765200	Enhancers	Primary T cells fromperipheralblood	blood
13	chr12:10764200-10765200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:10764200-10765200	Weak transcription	Spleen	Spleen
15	chr12:10764400-10765400	Transcr. at gene 5' and 3'	Dnd41	blood
16	chr12:10764400-10765600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:10764600-10765200	Enhancers	Primary B cells from cord blood	blood
18	chr12:10764600-10765200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr12:10764600-10765200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr12:10764600-10765200	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr12:10764600-10765200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:10764600-10765200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:10764600-10765200	Enhancers	Colon Smooth Muscle	Colon
24	chr12:10764600-10765400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:10764600-10765400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:10764600-10765400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr12:10764600-10765400	Enhancers	Primary B cells from peripheral blood	blood
28	chr12:10764600-10765400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:10764600-10765400	Enhancers	Small Intestine	intestine
30	chr12:10764600-10765400	Flanking Active TSS	Hela-S3	cervix
31	chr12:10764600-10765600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:10764600-10765600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:10764600-10765600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr12:10764600-10765600	Transcr. at gene 5' and 3'	A549	lung
35	chr12:10764600-10765600	Flanking Active TSS	HMEC	breast
36	chr12:10764600-10765600	Flanking Active TSS	HUVEC	blood vessel
37	chr12:10764600-10765600	Flanking Active TSS	Osteobl	bone
38	chr12:10764600-10765800	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr12:10764600-10765800	Flanking Active TSS	Liver	Liver
40	chr12:10764600-10765800	Flanking Active TSS	Fetal Brain Female	brain
41	chr12:10764600-10766800	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr12:10764600-10766800	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr12:10764600-10767000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:10764600-10767200	Active TSS	K562	blood
45	chr12:10764800-10765200	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr12:10764800-10765200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr12:10764800-10765200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:10764800-10765200	Enhancers	Brain Substantia Nigra	brain
49	chr12:10764800-10765200	Flanking Active TSS	Fetal Brain Male	brain
50	chr12:10764800-10765200	Enhancers	Fetal Heart	heart

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