Variant report

Variant	rs10257135
Chromosome Location	chr7:104893565-104893566
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:104893338..104895687-chr7:104903857..104906194,3	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10238507	0.96[LWK][hapmap]
rs10953470	0.90[YRI][hapmap];0.91[AFR][1000 genomes]
rs10953474	0.91[AFR][1000 genomes]
rs11765899	0.87[AFR][1000 genomes]
rs1204056	0.89[LWK][hapmap];1.00[YRI][hapmap]
rs1204058	1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1204066	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs1204077	1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs1204080	1.00[YRI][hapmap]
rs12334245	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs2030776	1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap]
rs2385537	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap]
rs3779210	0.96[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs3801278	1.00[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs3801281	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs3801282	1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs4496901	0.90[AFR][1000 genomes]
rs4730074	1.00[JPT][hapmap]
rs4730076	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6466053	1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6466057	1.00[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6466064	0.85[LWK][hapmap]
rs66599006	0.91[AFR][1000 genomes]
rs6962856	0.81[AFR][1000 genomes]
rs6967587	0.89[YRI][hapmap]
rs7357199	1.00[YRI][hapmap]
rs7806591	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs917114	1.00[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9640686	0.88[AFR][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	esv34588	chr7:104737612-105153242	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv2757233	chr7:104758250-105208492	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv2759549	chr7:104758250-105208492	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv8196	chr7:104763559-105155978	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv34580	chr7:104763580-105153242	Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription 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	15 gene(s)	inside rSNPs	diseases
6	esv2758127	chr7:104766707-105110581	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1028228	chr7:104807207-105182998	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv932138	chr7:104826194-105152816	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1015688	chr7:104849770-105182998	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10257135	ATXN7L1	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104869600-104909200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:104872200-104897200	Weak transcription	Primary T cells from cord blood	blood
3	chr7:104875000-104893800	Genic enhancers	Dnd41	blood
4	chr7:104877200-104898400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr7:104879000-104907800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:104879600-104897400	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr7:104879800-104896800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:104885400-104907000	Weak transcription	Fetal Intestine Small	intestine
9	chr7:104886000-104902200	Weak transcription	Lung	lung
10	chr7:104886400-104916600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:104886600-104895200	Weak transcription	Pancreas	Pancrea
12	chr7:104886600-104896800	Weak transcription	Right Atrium	heart
13	chr7:104886800-104898000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr7:104887000-104897200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr7:104887200-104897400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr7:104887400-104893800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr7:104887400-104896800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr7:104887600-104897200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr7:104887600-104897200	Weak transcription	HSMM	muscle
20	chr7:104887800-104895800	Weak transcription	Thymus	Thymus
21	chr7:104887800-104897200	Weak transcription	K562	blood
22	chr7:104887800-104897400	Weak transcription	Fetal Heart	heart
23	chr7:104888000-104897400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr7:104889400-104894000	Enhancers	Brain Cingulate Gyrus	brain
25	chr7:104889400-104896800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr7:104889600-104896000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:104889600-104902200	Weak transcription	HMEC	breast
28	chr7:104889800-104896200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr7:104890200-104894800	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr7:104890200-104897600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr7:104890400-104897600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr7:104890800-104895000	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr7:104890800-104896200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr7:104891200-104894800	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr7:104891400-104895000	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr7:104891400-104897200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr7:104891600-104893800	Weak transcription	HSMMtube	muscle
38	chr7:104891600-104895800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr7:104891600-104896400	Weak transcription	Primary B cells from cord blood	blood
40	chr7:104891600-104896800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr7:104891600-104907800	Weak transcription	Aorta	Aorta
42	chr7:104891800-104894200	Enhancers	Fetal Thymus	thymus
43	chr7:104891800-104896800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr7:104892200-104897000	Weak transcription	Brain Angular Gyrus	brain
45	chr7:104892200-104897200	Weak transcription	Brain Anterior Caudate	brain
46	chr7:104892200-104897200	Weak transcription	Brain Germinal Matrix	brain
47	chr7:104892200-104897200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr7:104892200-104897400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr7:104892200-104906600	Weak transcription	Colon Smooth Muscle	Colon
50	chr7:104892400-104893600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links