Variant report

Variant	rs11111981
Chromosome Location	chr12:104684773-104684774
allele	A/C
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	SP1	chr12:104684585-104685109	A549	lung:	n/a	n/a
2	POLR2A	chr12:104684652-104684857	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:104684492-104684833	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr12:104684563-104684919	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr12:104684617-104685037	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr12:104684682-104705657	A549	lung:	n/a	n/a
7	REST	chr12:104684562-104685008	A549	lung:	n/a	n/a
8	POLR2A	chr12:104684703-104684931	Hela-S3	cervix:	n/a	n/a
9	GATA3	chr12:104679262-104685085	A549	lung:	n/a	chr12:104683188-104683204 chr12:104683192-104683201 chr12:104683191-104683199 chr12:104683216-104683229 chr12:104683841-104683851 chr12:104683193-104683210
10	POLR2A	chr12:104684758-104684930	A549	lung:	n/a	n/a
11	TCF12	chr12:104679345-104685076	A549	lung:	n/a	chr12:104683753-104683760
12	POLR2A	chr12:104684716-104685024	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr12:104684730-104684921	Hela-S3	cervix:	n/a	n/a
14	CEBPB	chr12:104684072-104684898	A549	lung:	n/a	chr12:104684427-104684438

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104606650..104616346-chr12:104679108..104687347,18	K562	blood:

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

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10778321	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861187	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861190	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10861193	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861195	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861196	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861197	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861198	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861199	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861208	0.89[ASN][1000 genomes]
rs11111979	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111980	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111984	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111987	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111995	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111996	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112006	0.92[ASN][1000 genomes]
rs11609469	0.89[ASN][1000 genomes]
rs12811618	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17202060	0.98[ASN][1000 genomes]
rs17202520	0.92[ASN][1000 genomes]
rs4075411	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4595619	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4601859	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964782	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964783	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964785	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5018287	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132675	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7294778	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298739	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7488680	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977410	0.94[ASN][1000 genomes]
rs7977553	0.92[ASN][1000 genomes]
rs7978051	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11111981	EID3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104682000-104687400	Transcr. at gene 5' and 3'	A549	lung
2	chr12:104682600-104685000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:104682800-104685000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr12:104683000-104685600	Weak transcription	Small Intestine	intestine
5	chr12:104683000-104686000	Transcr. at gene 5' and 3'	HUVEC	blood vessel
6	chr12:104683200-104687400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:104683400-104686600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:104683400-104687800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
9	chr12:104683400-104688600	Weak transcription	Brain Substantia Nigra	brain
10	chr12:104683400-104696800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:104683600-104684800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:104683600-104689000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr12:104683600-104690200	Weak transcription	Fetal Kidney	kidney
14	chr12:104683800-104684800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:104683800-104684800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:104683800-104684800	Weak transcription	Liver	Liver
17	chr12:104683800-104684800	Active TSS	NHLF	lung
18	chr12:104683800-104685000	Active TSS	Right Ventricle	heart
19	chr12:104683800-104685400	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr12:104683800-104685400	Weak transcription	Fetal Muscle Leg	muscle
21	chr12:104683800-104685400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:104683800-104685400	Weak transcription	HSMM	muscle
23	chr12:104683800-104685600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr12:104683800-104685600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr12:104683800-104685600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:104683800-104685600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:104683800-104685600	Weak transcription	Adipose Nuclei	Adipose
28	chr12:104683800-104685600	Weak transcription	Brain Hippocampus Middle	brain
29	chr12:104683800-104685600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr12:104683800-104685600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr12:104683800-104685600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr12:104683800-104685600	Weak transcription	Fetal Intestine Large	intestine
33	chr12:104683800-104685600	Weak transcription	Fetal Lung	lung
34	chr12:104683800-104685800	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr12:104683800-104685800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:104683800-104685800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:104683800-104685800	Weak transcription	Colonic Mucosa	Colon
38	chr12:104683800-104685800	Weak transcription	Thymus	Thymus
39	chr12:104683800-104685800	Weak transcription	HSMMtube	muscle
40	chr12:104683800-104686000	Weak transcription	Aorta	Aorta
41	chr12:104683800-104686400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr12:104683800-104686400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr12:104683800-104686600	Strong transcription	NHDF-Ad	bronchial
44	chr12:104683800-104686800	Strong transcription	Fetal Intestine Small	intestine
45	chr12:104683800-104686800	Weak transcription	Psoas Muscle	Psoas
46	chr12:104683800-104687000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr12:104683800-104688400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:104683800-104688600	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr12:104683800-104688800	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr12:104683800-104688800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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