Variant report

Variant	rs11111987
Chromosome Location	chr12:104698582-104698583
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF3	chr12:104696811-104698807	A549	lung:	n/a	n/a
2	SP1	chr12:104696322-104698630	A549	lung:	n/a	n/a
3	FOSL2	chr12:104696444-104698901	A549	lung:	n/a	n/a
4	POLR2A	chr12:104698582-104698762	HUVEC	blood vessel:	n/a	n/a
5	SIN3AK20	chr12:104697462-104698781	A549	lung:	n/a	n/a
6	USF2	chr12:104697964-104698963	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr12:104696416-104698790	HUVEC	blood vessel:	n/a	n/a
8	ETS1	chr12:104697062-104698857	A549	lung:	n/a	chr12:104697900-104697907 chr12:104697692-104697703 chr12:104697872-104697881
9	SP1	chr12:104695282-104698790	A549	lung:	n/a	n/a
10	MAX	chr12:104696465-104698833	A549	lung:	n/a	chr12:104698605-104698614
11	TCF12	chr12:104695268-104701849	A549	lung:	n/a	n/a
12	POLR2A	chr12:104696354-104701825	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr12:104696544-104702660	HepG2	liver:	n/a	n/a
14	CEBPB	chr12:104698219-104698818	A549	lung:	n/a	n/a
15	POLR2A	chr12:104684682-104705657	A549	lung:	n/a	n/a
16	SIX5	chr12:104695288-104701950	A549	lung:	n/a	chr12:104700345-104700361 chr12:104699538-104699547 chr12:104698479-104698493 chr12:104700866-104700882
17	REST	chr12:104696446-104701824	A549	lung:	n/a	chr12:104698081-104698101 chr12:104697868-104697886 chr12:104698081-104698101 chr12:104698082-104698100 chr12:104698081-104698101
18	CEBPB	chr12:104698158-104698729	A549	lung:	n/a	n/a
19	POLR2A	chr12:104697825-104698812	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr12:104696471-104698728	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr12:104696555-104698600	Hela-S3	cervix:	n/a	n/a
22	E2F6	chr12:104697060-104698610	A549	lung:	n/a	n/a
23	BCL3	chr12:104696506-104698772	A549	lung:	n/a	chr12:104697692-104697701 chr12:104697695-104697704
24	MXI1	chr12:104696857-104698994	IMR90	lung:	n/a	n/a
25	POLR2A	chr12:104696376-104698758	Hela-S3	cervix:	n/a	n/a
26	BCL3	chr12:104696463-104700456	A549	lung:	n/a	chr12:104697692-104697701 chr12:104697695-104697704
27	POLR2A	chr12:104697466-104698697	K562	blood:	n/a	n/a
28	GATA3	chr12:104696427-104698835	A549	lung:	n/a	chr12:104696608-104696620 chr12:104696600-104696617 chr12:104696609-104696618 chr12:104696611-104696618 chr12:104696609-104696619
29	POLR2A	chr12:104695319-104698854	PANC-1	pancreas:	n/a	n/a
30	POLR2A	chr12:104697535-104699689	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:104696590..104698591-chr12:104702374..104705113,2	MCF-7	breast:
2	chr12:104698485..104699359-chr18:60383210..60383734,2	MCF-7	breast:
3	chr12:104680142..104683904-chr12:104694272..104698636,5	MCF-7	breast:

Variant related genes	Relation type
TXNRD1	TF binding region
ENSG00000198431	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10778321	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10861185	0.85[CEU][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs10861187	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10861190	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10861193	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10861195	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10861196	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10861197	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10861198	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10861199	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10861208	0.89[ASN][1000 genomes]
rs11111938	0.85[JPT][hapmap]
rs11111940	0.86[JPT][hapmap]
rs11111945	0.81[JPT][hapmap]
rs11111960	0.91[GIH][hapmap]
rs11111979	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111980	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111981	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111984	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111995	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111996	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112006	0.91[ASN][1000 genomes]
rs11609469	0.89[ASN][1000 genomes]
rs12811618	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17202060	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17202520	0.91[ASN][1000 genomes]
rs4075411	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4445711	0.86[JPT][hapmap]
rs4595619	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4601859	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964782	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4964783	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4964785	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5018287	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7132675	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7294778	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7297956	0.82[JPT][hapmap]
rs7298739	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7310815	0.81[JPT][hapmap]
rs7488680	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7954970	0.84[JPT][hapmap]
rs7958262	0.86[JPT][hapmap]
rs7977410	0.94[ASN][1000 genomes]
rs7977553	0.91[ASN][1000 genomes]
rs7978051	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats 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
3	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1048075	chr12:104694799-104751460	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv541588	chr12:104694799-104751460	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv52994	chr12:104696286-104701777	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11111987	EID3	cis	Adipose Subcutaneous	GTEx
rs11111987	TCP11L2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104683800-104723800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:104686200-104700600	Strong transcription	Dnd41	blood
3	chr12:104687200-104700600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:104691200-104702200	Transcr. at gene 5' and 3'	A549	lung
5	chr12:104691800-104703400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:104695800-104700800	Strong transcription	K562	blood
7	chr12:104696600-104701600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:104696800-104698800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr12:104696800-104699200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:104697200-104700000	Strong transcription	HepG2	liver
11	chr12:104697200-104706200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr12:104697600-104698600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr12:104697600-104698600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:104697600-104698600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:104697600-104698600	Flanking Active TSS	GM12878-XiMat	blood
16	chr12:104697600-104698600	Transcr. at gene 5' and 3'	NHLF	lung
17	chr12:104697800-104698600	Genic enhancers	HUES48 Cell Line	embryonic stem cell
18	chr12:104697800-104698600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
19	chr12:104697800-104698600	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr12:104697800-104698600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr12:104697800-104698600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr12:104697800-104698600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:104697800-104698600	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr12:104697800-104698600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr12:104697800-104698600	Flanking Active TSS	Rectal Smooth Muscle	rectum
26	chr12:104698000-104698600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:104698000-104698600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr12:104698000-104698600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr12:104698000-104698600	Flanking Active TSS	Fetal Stomach	stomach
30	chr12:104698000-104698600	Enhancers	Small Intestine	intestine
31	chr12:104698000-104698600	Strong transcription	HSMMtube	muscle
32	chr12:104698000-104698800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
33	chr12:104698000-104699200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:104698000-104699200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr12:104698000-104699600	Weak transcription	Lung	lung
36	chr12:104698000-104700000	Enhancers	Right Ventricle	heart
37	chr12:104698000-104703000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:104698000-104703400	Weak transcription	Left Ventricle	heart
39	chr12:104698000-104704000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:104698000-104705000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:104698000-104707400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr12:104698000-104707600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr12:104698000-104707800	Weak transcription	Esophagus	oesophagus
44	chr12:104698000-104711400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:104698000-104716200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr12:104698200-104698600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:104698200-104698800	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr12:104698200-104699200	Weak transcription	Aorta	Aorta
49	chr12:104698200-104699400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:104698200-104699400	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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