Variant report

Variant	rs4423787
Chromosome Location	chr3:67512114-67512115
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs4258984	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4320072	0.84[ASW][hapmap];0.82[YRI][hapmap]
rs4479607	0.82[EUR][1000 genomes]
rs4856867	0.89[EUR][1000 genomes]
rs6548593	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6792584	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7616397	0.86[EUR][1000 genomes]
rs7628838	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7645087	0.80[EUR][1000 genomes]
rs9810030	0.89[EUR][1000 genomes]
rs9815209	0.80[EUR][1000 genomes]
rs9818109	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9836548	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851569	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9856294	0.83[EUR][1000 genomes]
rs9873214	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007093	chr3:67113534-67602973	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv470638	chr3:67367341-67814738	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv460700	chr3:67393629-67712970	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv590560	chr3:67393629-67712970	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv834719	chr3:67396626-67589852	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv3860	chr3:67493286-67517941	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4423787	ATXN7	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67435600-67534200	Weak transcription	Aorta	Aorta
2	chr3:67471600-67518800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:67473400-67521000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr3:67473600-67542000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr3:67478200-67512200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:67482600-67527200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:67482600-67528600	Weak transcription	GM12878-XiMat	blood
8	chr3:67482800-67520800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr3:67482800-67533400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:67487000-67518600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:67487800-67512200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:67488000-67544200	Weak transcription	A549	lung
13	chr3:67488400-67566400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:67492200-67545400	Weak transcription	Fetal Intestine Small	intestine
15	chr3:67492400-67515400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr3:67492400-67516600	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr3:67498000-67534200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:67500800-67567000	Weak transcription	Pancreas	Pancrea
19	chr3:67501200-67533600	Weak transcription	Fetal Intestine Large	intestine
20	chr3:67504000-67559800	Weak transcription	Esophagus	oesophagus
21	chr3:67504600-67518800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:67504800-67513400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:67505800-67516200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:67506200-67512800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:67506600-67544000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr3:67508200-67577600	Weak transcription	Spleen	Spleen
27	chr3:67508800-67542000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:67509000-67537200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr3:67509200-67534400	Weak transcription	Left Ventricle	heart
30	chr3:67509600-67512600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:67509800-67512200	Weak transcription	Fetal Heart	heart
32	chr3:67509800-67513600	Strong transcription	Liver	Liver
33	chr3:67510000-67515600	Strong transcription	Primary B cells from cord blood	blood
34	chr3:67510400-67512200	Weak transcription	Ovary	ovary
35	chr3:67510400-67512600	Weak transcription	Primary T cells from cord blood	blood
36	chr3:67510800-67513400	Enhancers	HUVEC	blood vessel
37	chr3:67511000-67513400	Enhancers	NHLF	lung
38	chr3:67511400-67512800	Enhancers	Fetal Kidney	kidney
39	chr3:67511400-67512800	Enhancers	Fetal Lung	lung
40	chr3:67511400-67513600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:67511400-67513600	Enhancers	NHDF-Ad	bronchial
42	chr3:67511400-67514400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:67511600-67513000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:67511600-67560000	Weak transcription	Lung	lung
45	chr3:67511800-67513000	Enhancers	Fetal Stomach	stomach
46	chr3:67511800-67513200	Enhancers	HSMMtube	muscle
47	chr3:67511800-67514400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:67511800-67565000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr3:67512000-67512200	Enhancers	Adipose Nuclei	Adipose
50	chr3:67512000-67512200	Flanking Active TSS	HSMM	muscle

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