Variant report

Variant	rs11111797
Chromosome Location	chr12:104208972-104208973
allele	A/T
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	GATA3	chr12:104207586-104209433	SK-N-SH	brain:	n/a	chr12:104208559-104208566 chr12:104208700-104208711 chr12:104208554-104208570 chr12:104208559-104208566 chr12:104208183-104208193 chr12:104208556-104208568 chr12:104208559-104208566
2	TCF12	chr12:104207659-104209377	SK-N-SH	brain:	n/a	n/a
3	PBX3	chr12:104208908-104209332	SK-N-SH	brain:	n/a	n/a
4	JUND	chr12:104208105-104209235	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr12:104207968-104209251	SK-N-SH	brain:	n/a	n/a
6	NFIC	chr12:104207689-104209292	SK-N-SH	brain:	n/a	n/a
7	FOSL2	chr12:104208104-104209114	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr12:104207678-104209474	SK-N-SH	brain:	n/a	chr12:104208559-104208566 chr12:104208700-104208711 chr12:104208554-104208570 chr12:104208559-104208566 chr12:104208183-104208193 chr12:104208556-104208568 chr12:104208559-104208566

No.	Distal block	Cell Line	Cell type
1	chr12:104208263..104213427-chr12:104233273..104236383,5	K562	blood:
2	chr12:104202254..104204379-chr12:104208308..104210775,2	MCF-7	breast:
3	chr12:104208479..104212455-chr12:104217163..104218930,3	MCF-7	breast:
4	chr12:104207954..104212094-chr12:104233273..104237214,4	K562	blood:
5	chr12:104200580..104204661-chr12:104208067..104211223,3	K562	blood:

Variant related genes	Relation type
ENSG00000257754	TF binding region
ENSG00000257327	Chromatin interaction
ENSG00000111696	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10082821	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10778288	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10778289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10861110	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10861111	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10861113	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861114	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10861115	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10861116	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10861117	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10861118	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10861119	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11111760	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs11111780	1.00[CHB][hapmap]
rs11111790	1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11111794	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11111802	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs11111803	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11111806	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11111807	0.94[EUR][1000 genomes]
rs12299784	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12313259	0.89[CEU][hapmap]
rs12320424	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12368209	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs12369835	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12426059	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1370782	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1370783	0.93[EUR][1000 genomes]
rs17034657	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs3087891	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs4964197	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4964540	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4964571	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4964574	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4964605	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4964787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6539102	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7138889	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs7315948	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73175816	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899480	chr12:104092996-104211440	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv899481	chr12:104092996-104213731	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899482	chr12:104092996-104218956	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv899483	chr12:104117462-104218956	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv899487	chr12:104118587-104218956	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv899489	chr12:104144835-104218956	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv899490	chr12:104149022-104218956	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11111797	RP11-341G23.4	cis	Whole Blood	GTEx
rs11111797	NT5DC3	cis	Whole Blood	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104171800-104216000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr12:104187800-104212600	Weak transcription	GM12878-XiMat	blood
3	chr12:104191000-104209800	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr12:104191000-104211800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr12:104193000-104217600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:104194600-104214600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:104194600-104214800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr12:104194800-104215200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr12:104195000-104213800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:104196400-104213600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr12:104196400-104214800	Weak transcription	Brain Substantia Nigra	brain
12	chr12:104196400-104221800	Weak transcription	Brain Anterior Caudate	brain
13	chr12:104196600-104212800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:104196600-104213000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:104199200-104211000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:104199200-104211800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr12:104199600-104214600	Weak transcription	Esophagus	oesophagus
18	chr12:104200000-104214600	Weak transcription	Ovary	ovary
19	chr12:104200200-104216200	Weak transcription	NHDF-Ad	bronchial
20	chr12:104200400-104210000	Weak transcription	Hela-S3	cervix
21	chr12:104201000-104214600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:104201400-104209000	Weak transcription	HUVEC	blood vessel
23	chr12:104201400-104214800	Weak transcription	NHLF	lung
24	chr12:104201600-104212600	Weak transcription	Psoas Muscle	Psoas
25	chr12:104202200-104209400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:104202200-104218200	Weak transcription	Gastric	stomach
27	chr12:104202400-104214800	Weak transcription	Brain Hippocampus Middle	brain
28	chr12:104203600-104209200	Strong transcription	NHEK	skin
29	chr12:104204000-104209200	Strong transcription	Primary T cells from cord blood	blood
30	chr12:104204000-104214600	Weak transcription	Fetal Intestine Small	intestine
31	chr12:104205800-104214600	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr12:104206800-104209400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr12:104207200-104212600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:104207200-104215400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr12:104207400-104217200	Weak transcription	Fetal Intestine Large	intestine
36	chr12:104207600-104209000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr12:104207600-104214600	Weak transcription	Fetal Muscle Leg	muscle
38	chr12:104208000-104209200	Weak transcription	Aorta	Aorta
39	chr12:104208000-104212600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:104208000-104213800	Weak transcription	HSMM	muscle
41	chr12:104208000-104214600	Weak transcription	Lung	lung
42	chr12:104208000-104214800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr12:104208000-104215000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr12:104208000-104215000	Weak transcription	NH-A	brain
45	chr12:104208200-104209400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:104208200-104210000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr12:104208200-104210000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr12:104208200-104210000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr12:104208200-104211000	Weak transcription	Liver	Liver
50	chr12:104208200-104211000	Weak transcription	Fetal Lung	lung

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