Variant report

Variant	rs7042576
Chromosome Location	chr9:101012594-101012595
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100986946..100989189-chr9:101010558..101012631,2	MCF-7	breast:
2	chr9:100955094..100957753-chr9:101010315..101013161,2	MCF-7	breast:
3	chr9:101010838..101012752-chr9:101014329..101016410,2	MCF-7	breast:
4	chr9:100842559..100845315-chr9:101012488..101014157,2	MCF-7	breast:
5	chr9:101010177..101013807-chr9:101023006..101027119,4	K562	blood:
6	chr9:101005587..101007898-chr9:101011469..101013243,2	MCF-7	breast:
7	chr9:100965216..100966924-chr9:101011389..101013937,2	K562	blood:
8	chr9:101010268..101015223-chr9:101016008..101021084,8	K562	blood:
9	chr17:62493356..62496289-chr9:101011192..101012873,2	MCF-7	breast:
10	chr9:101011351..101016361-chr9:101016435..101019100,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000095383	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10115971	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10120564	0.82[AFR][1000 genomes]
rs10123643	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10124977	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10760210	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760216	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10760217	0.93[ASN][1000 genomes]
rs10760218	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10818627	0.93[ASN][1000 genomes]
rs10818640	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	0.93[ASN][1000 genomes]
rs10818648	0.90[ASN][1000 genomes]
rs10818656	0.90[ASN][1000 genomes]
rs10818658	0.93[ASN][1000 genomes]
rs10818662	0.85[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs10818666	0.93[ASN][1000 genomes]
rs10818667	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818668	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818672	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	0.81[CEU][hapmap];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	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10985580	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[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	0.89[AMR][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	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4742719	0.93[ASN][1000 genomes]
rs4743187	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4743188	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]
rs4743192	0.90[ASN][1000 genomes]
rs4743194	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5010004	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs55705027	0.80[AFR][1000 genomes]
rs62574277	0.90[ASN][1000 genomes]
rs6478630	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478631	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs67569753	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025781	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7032046	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7045158	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7853442	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7853847	1.00[JPT][hapmap]
rs7868451	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7873849	0.90[ASN][1000 genomes]
rs879368	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs879369	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
rs7042576	TBC1D2	cis	Thyroid	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100989600-101016000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:100991400-101015400	Weak transcription	Brain Anterior Caudate	brain
3	chr9:100992200-101012800	Weak transcription	Brain Substantia Nigra	brain
4	chr9:100992200-101016000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr9:100993400-101012600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr9:100995000-101016600	Weak transcription	Brain Angular Gyrus	brain
7	chr9:100996000-101016000	Weak transcription	Pancreas	Pancrea
8	chr9:100996200-101017200	Weak transcription	Ovary	ovary
9	chr9:101004200-101015800	Weak transcription	Brain Hippocampus Middle	brain
10	chr9:101004200-101017200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr9:101005200-101017200	Weak transcription	Brain Germinal Matrix	brain
12	chr9:101006400-101014000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:101006600-101014000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:101006600-101016600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr9:101006800-101016800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr9:101007000-101013800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr9:101008000-101012600	Weak transcription	HepG2	liver
18	chr9:101008800-101013600	Enhancers	Placenta	Placenta
19	chr9:101008800-101013800	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr9:101009000-101017200	Weak transcription	Aorta	Aorta
21	chr9:101009200-101015800	Weak transcription	Stomach Mucosa	stomach
22	chr9:101009200-101016600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr9:101009400-101012600	Enhancers	Primary hematopoietic stem cells	blood
24	chr9:101010200-101012600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:101010200-101012600	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr9:101010200-101013400	Genic enhancers	HMEC	breast
27	chr9:101010200-101014000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr9:101010200-101014200	Genic enhancers	Osteobl	bone
29	chr9:101010200-101015000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr9:101010200-101015200	Enhancers	A549	lung
31	chr9:101010200-101015600	Enhancers	NHDF-Ad	bronchial
32	chr9:101010200-101016600	Enhancers	Primary B cells from cord blood	blood
33	chr9:101010400-101012800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr9:101010400-101013000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr9:101010400-101013000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:101010400-101013000	Enhancers	Right Atrium	heart
37	chr9:101010400-101013000	Genic enhancers	NHLF	lung
38	chr9:101010400-101013200	Enhancers	Colonic Mucosa	Colon
39	chr9:101010400-101013200	Genic enhancers	HSMMtube	muscle
40	chr9:101010400-101014000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr9:101010400-101014000	Genic enhancers	HSMM	muscle
42	chr9:101010400-101014600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr9:101010400-101014600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr9:101010400-101014600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
45	chr9:101010400-101014800	Genic enhancers	Lung	lung
46	chr9:101010600-101012800	Genic enhancers	Fetal Intestine Large	intestine
47	chr9:101010600-101015400	Genic enhancers	Fetal Intestine Small	intestine
48	chr9:101010600-101017200	Enhancers	Placenta Amnion	Placenta Amnion
49	chr9:101011000-101012600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr9:101011000-101012600	Strong transcription	Brain Cingulate Gyrus	brain

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