Variant report

Variant	rs2742243
Chromosome Location	chr10:43601749-43601750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43601071..43602866-chr10:43603676..43605812,2	K562	blood:
2	chr10:43589765..43592695-chr10:43600961..43603100,2	MCF-7	breast:
3	chr10:43571287..43574219-chr10:43600622..43603596,3	MCF-7	breast:
4	chr10:43587904..43589717-chr10:43600959..43603478,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165731	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12767776	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1800858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1864401	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1864402	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1864403	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864404	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864408	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1864410	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2251674	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435344	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2435356	0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2435357	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2435358	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2435359	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2435362	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2435366	0.88[ASN][1000 genomes]
rs2505533	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505535	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2505536	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2505537	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2505990	0.82[EUR][1000 genomes]
rs2505991	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2505994	0.83[EUR][1000 genomes]
rs2505998	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2506004	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2506005	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2506006	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2506008	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2565203	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2565204	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742237	0.83[CHB][hapmap]
rs2742244	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28502801	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28576059	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7092603	0.84[EUR][1000 genomes]
rs752977	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050394	chr10:42890663-43604956	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv540573	chr10:42890663-43604956	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	nsv1038102	chr10:43441601-43642908	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv466880	chr10:43452436-43616751	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
7	nsv550695	chr10:43452436-43616751	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
8	nsv895082	chr10:43530071-43755506	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv895083	chr10:43549708-43765485	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv1051701	chr10:43555542-43642895	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
11	nsv522592	chr10:43574936-43615505	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv522566	chr10:43596728-43610671	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43601000-43601800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
2	chr10:43601000-43601800	Bivalent Enhancer	Placenta	Placenta
3	chr10:43601000-43601800	Weak transcription	HUVEC	blood vessel
4	chr10:43601000-43602000	Enhancers	Primary B cells from cord blood	blood
5	chr10:43601000-43602000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr10:43601000-43602600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr10:43601000-43605800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr10:43601200-43602000	Enhancers	Fetal Intestine Large	intestine
9	chr10:43601200-43602200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
10	chr10:43601200-43602400	Enhancers	Primary B cells from peripheral blood	blood
11	chr10:43601200-43602600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr10:43601200-43603000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr10:43601400-43601800	Enhancers	Fetal Intestine Small	intestine
14	chr10:43601400-43601800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
15	chr10:43601400-43602000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr10:43601400-43602000	Enhancers	Colonic Mucosa	Colon
17	chr10:43601400-43602200	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr10:43601400-43602200	Enhancers	Primary T cells fromperipheralblood	blood
19	chr10:43601400-43602200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr10:43601400-43602400	Enhancers	Spleen	Spleen
21	chr10:43601400-43602400	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr10:43601400-43602800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr10:43601400-43604200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr10:43601400-43604800	Weak transcription	NHEK	skin
25	chr10:43601400-43605000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr10:43601400-43605200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr10:43601400-43605400	Weak transcription	NHDF-Ad	bronchial
28	chr10:43601400-43605600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr10:43601400-43605600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr10:43601400-43605600	Weak transcription	Fetal Lung	lung
31	chr10:43601400-43605600	Weak transcription	HSMM	muscle
32	chr10:43601400-43605800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr10:43601400-43605800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr10:43601400-43605800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr10:43601400-43605800	Weak transcription	GM12878-XiMat	blood
36	chr10:43601400-43605800	Weak transcription	HMEC	breast
37	chr10:43601400-43606000	Weak transcription	Right Atrium	heart
38	chr10:43601400-43613400	Weak transcription	Liver	Liver
39	chr10:43601400-43632800	Weak transcription	Gastric	stomach
40	chr10:43601600-43601800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr10:43601600-43604400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr10:43601600-43604600	Weak transcription	Fetal Muscle Leg	muscle
43	chr10:43601600-43604800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr10:43601600-43605000	Weak transcription	Pancreas	Pancrea
45	chr10:43601600-43605400	Weak transcription	Fetal Thymus	thymus
46	chr10:43601600-43605600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr10:43601600-43605600	Weak transcription	Ovary	ovary
48	chr10:43601600-43606000	Weak transcription	Esophagus	oesophagus
49	chr10:43601600-43606000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr10:43601600-43606200	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links