Variant report

Variant	rs4630370
Chromosome Location	chr12:105346800-105346801
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr12:105346632-105347486	A549	lung:	n/a	n/a
2	TCF12	chr12:105346450-105347604	A549	lung:	n/a	n/a
3	TAL1	chr12:105346589-105346880	K562	blood:	n/a	n/a
4	MAX	chr12:105346602-105346820	NB4	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:105343851..105348812-chr12:105350003..105354386,8	MCF-7	breast:
2	chr12:105345347..105347103-chr12:105350407..105353151,2	MCF-7	breast:
3	chr12:105345942..105347819-chr12:105351502..105353153,2	K562	blood:
4	chr12:105344565..105347442-chr12:105349621..105353002,3	K562	blood:

No data

Variant related genes	Relation type
SLC41A2	TF binding region
ENSG00000136052	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10507183	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs10507185	0.89[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10778354	0.89[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10778356	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10861278	0.85[ASN][1000 genomes]
rs10861280	0.82[ASN][1000 genomes]
rs10861282	0.89[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861291	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10861293	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861295	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10861297	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112208	0.88[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs11112221	0.86[ASN][1000 genomes]
rs11112234	0.89[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12230637	0.88[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs17829927	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2047126	0.84[ASN][1000 genomes]
rs2245695	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2249941	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2252843	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2264883	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2264893	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2453163	0.86[ASN][1000 genomes]
rs2453164	0.86[ASN][1000 genomes]
rs2453169	0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs2463430	0.81[ASN][1000 genomes]
rs2468088	0.80[ASN][1000 genomes]
rs2468094	0.82[ASN][1000 genomes]
rs2468096	0.85[ASN][1000 genomes]
rs2468098	0.85[ASN][1000 genomes]
rs2468103	0.86[ASN][1000 genomes]
rs2468107	0.88[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2468108	0.86[ASN][1000 genomes]
rs2468336	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2468338	0.88[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2468339	0.88[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs2468341	0.88[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2468342	0.82[ASN][1000 genomes]
rs2468343	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs2468344	0.80[ASN][1000 genomes]
rs2468345	0.82[ASN][1000 genomes]
rs2468396	0.86[EUR][1000 genomes]
rs2468397	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2642119	0.86[ASN][1000 genomes]
rs2642120	0.94[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs2730294	0.88[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs3890816	0.96[CEU][hapmap]
rs4130161	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4257060	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4409923	0.89[CEU][hapmap]
rs4537841	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4644704	0.89[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57987047	0.91[EUR][1000 genomes]
rs7959777	0.89[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7961766	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7971260	0.86[ASN][1000 genomes]
rs7971392	0.88[ASN][1000 genomes]
rs9705471	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4630370	C12orf23	cis	parietal	SCAN
rs4630370	GNPTAB	cis	parietal	SCAN
rs4630370	C12orf42	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105338200-105349000	Weak transcription	Pancreas	Pancrea
2	chr12:105338200-105351000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:105342600-105350600	Weak transcription	Adipose Nuclei	Adipose
4	chr12:105345400-105347800	Enhancers	HUVEC	blood vessel
5	chr12:105345600-105347800	Enhancers	Hela-S3	cervix
6	chr12:105346000-105346800	Enhancers	Small Intestine	intestine
7	chr12:105346000-105348200	Flanking Active TSS	A549	lung
8	chr12:105346200-105347400	Enhancers	HepG2	liver
9	chr12:105346400-105346800	Flanking Active TSS	Duodenum Mucosa	Duodenum
10	chr12:105346400-105347200	Active TSS	Aorta	Aorta
11	chr12:105346400-105347200	Enhancers	Fetal Kidney	kidney
12	chr12:105346400-105348400	Enhancers	Stomach Mucosa	stomach
13	chr12:105346600-105346800	Flanking Active TSS	Liver	Liver
14	chr12:105346600-105346800	Bivalent Enhancer	Fetal Intestine Large	intestine
15	chr12:105346600-105346800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr12:105346600-105347200	Bivalent Enhancer	Fetal Intestine Small	intestine
17	chr12:105346600-105347200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
18	chr12:105346600-105347400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:105346600-105347600	Enhancers	GM12878-XiMat	blood
20	chr12:105346800-105347000	Enhancers	Liver	Liver
21	chr12:105346800-105347200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:105346800-105347400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:105346800-105347600	Enhancers	Duodenum Mucosa	Duodenum
24	chr12:105346800-105347600	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr12:105346800-105351400	Weak transcription	Small Intestine	intestine

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