Variant report

Variant	rs4743188
Chromosome Location	chr9:100992695-100992696
allele	C/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	chr9:100992478-100992912	T-47D	breast:	n/a	chr9:100992660-100992667 chr9:100992659-100992667 chr9:100992660-100992667 chr9:100992660-100992667

No.	Distal block	Cell Line	Cell type
1	chr9:100991946..100993972-chr9:101018895..101020413,2	K562	blood:
2	chr9:100985570..100988965-chr9:100991767..100994360,5	MCF-7	breast:
3	chr9:100987506..100990430-chr9:100991998..100994397,3	K562	blood:
4	chr9:100991762..100993372-chr9:101000957..101003101,2	MCF-7	breast:
5	chr9:100991719..100993859-chr9:100997810..101000501,3	K562	blood:
6	chr9:100745757..100748081-chr9:100991742..100993945,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224001	TF binding region
TBC1D2	TF binding region
ENSG00000136938	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10115971	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10123643	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10124977	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10760210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760216	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10760217	0.93[ASN][1000 genomes]
rs10760218	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10818627	0.93[ASN][1000 genomes]
rs10818640	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10818644	0.93[ASN][1000 genomes]
rs10818645	0.93[ASN][1000 genomes]
rs10818646	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10818648	0.90[ASN][1000 genomes]
rs10818656	0.90[ASN][1000 genomes]
rs10818658	0.93[ASN][1000 genomes]
rs10818662	0.90[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs10818666	0.93[ASN][1000 genomes]
rs10818667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818668	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818672	0.86[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10818676	0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs10818677	0.90[ASN][1000 genomes]
rs10818678	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10818689	0.86[ASN][1000 genomes]
rs10818690	0.86[ASN][1000 genomes]
rs10818691	0.83[ASN][1000 genomes]
rs10818692	1.00[JPT][hapmap]
rs10818693	1.00[JPT][hapmap]
rs10818739	1.00[JPT][hapmap]
rs10818743	1.00[JPT][hapmap]
rs10985517	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10985580	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10985583	0.90[ASN][1000 genomes]
rs10985634	0.86[ASN][1000 genomes]
rs10985641	0.86[JPT][hapmap]
rs10985642	1.00[JPT][hapmap]
rs10985765	1.00[JPT][hapmap]
rs10985772	1.00[JPT][hapmap]
rs12237988	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12342612	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12346750	0.93[ASN][1000 genomes]
rs1435253	1.00[JPT][hapmap]
rs1435257	1.00[JPT][hapmap]
rs1573024	0.93[ASN][1000 genomes]
rs1573025	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17766883	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17766913	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1935389	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2900380	0.93[ASN][1000 genomes]
rs4379551	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4742719	0.93[ASN][1000 genomes]
rs4743187	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4743192	0.90[ASN][1000 genomes]
rs4743194	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5010004	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs62574277	0.90[ASN][1000 genomes]
rs6478630	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478631	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs67569753	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025781	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7032046	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7042576	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7045158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7853442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7853847	1.00[JPT][hapmap]
rs7868451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7873849	0.90[ASN][1000 genomes]
rs879368	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs879369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1053729	chr9:100909554-100997718	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv831663	chr9:100941048-101109492	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1045780	chr9:100943318-101080389	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540180	chr9:100943318-101080389	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4743188	TBC1D2	cis	Thyroid	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100955800-101003200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr9:100961400-101001400	Weak transcription	Right Atrium	heart
3	chr9:100968400-100995600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr9:100968400-100997600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr9:100968600-101010400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr9:100968800-100998000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:100968800-101011000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr9:100969400-101004800	Weak transcription	Brain Germinal Matrix	brain
9	chr9:100969600-100997200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:100970200-101001600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr9:100974800-101010600	Weak transcription	Colon Smooth Muscle	Colon
12	chr9:100976400-100998800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:100980200-101010200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr9:100981800-101010400	Weak transcription	Fetal Thymus	thymus
15	chr9:100982800-101004600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr9:100983000-101007200	Weak transcription	Fetal Brain Male	brain
17	chr9:100983200-100996600	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr9:100983200-100997600	Weak transcription	Fetal Brain Female	brain
19	chr9:100983400-101006200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:100983600-100994000	Weak transcription	Brain Angular Gyrus	brain
21	chr9:100985600-100998200	Genic enhancers	Fetal Intestine Small	intestine
22	chr9:100985800-100993200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:100985800-101002800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:100986000-100995400	Weak transcription	Pancreas	Pancrea
25	chr9:100986000-101006200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr9:100986200-100997600	Weak transcription	HUVEC	blood vessel
27	chr9:100986200-100998800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr9:100986200-100999000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr9:100987000-100993400	Enhancers	Liver	Liver
30	chr9:100987000-100995800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr9:100987000-100997200	Strong transcription	Lung	lung
32	chr9:100987000-100997800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr9:100987200-100992800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr9:100987200-100993400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:100987200-100993600	Genic enhancers	Placenta	Placenta
36	chr9:100987200-100996400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr9:100987200-100996800	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr9:100987200-100997400	Strong transcription	Primary T cells from cord blood	blood
39	chr9:100987400-100993200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr9:100987400-100994000	Strong transcription	Osteobl	bone
41	chr9:100987400-100996000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr9:100987600-100994000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr9:100987800-100992800	Strong transcription	NH-A	brain
44	chr9:100987800-100993600	Strong transcription	Thymus	Thymus
45	chr9:100987800-100994000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr9:100987800-100998200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr9:100988000-100994000	Strong transcription	Brain Hippocampus Middle	brain
48	chr9:100988200-100993800	Weak transcription	NHDF-Ad	bronchial
49	chr9:100988200-100994000	Strong transcription	HMEC	breast
50	chr9:100988200-100995800	Strong transcription	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links