Variant report

Variant	rs10002171
Chromosome Location	chr4:15767752-15767753
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10002394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10013987	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11930667	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11939567	0.93[ASN][1000 genomes]
rs12504480	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13116397	0.83[ASN][1000 genomes]
rs13116669	0.82[ASN][1000 genomes]
rs13120356	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13121175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13134405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16892396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16892407	0.93[ASN][1000 genomes]
rs34347605	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34689171	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35802132	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3796863	0.83[GIH][hapmap];0.86[JPT][hapmap]
rs4257648	0.91[ASN][1000 genomes]
rs4516711	0.86[JPT][hapmap]
rs4698417	0.92[ASN][1000 genomes]
rs4698420	0.86[JPT][hapmap]
rs68040828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6831585	0.90[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs6836946	0.83[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap]
rs6839601	0.93[ASN][1000 genomes]
rs6841880	0.83[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap]
rs6841924	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7681005	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv10460	chr4:15757611-15818206	ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2760884	chr4:15759680-15776181	Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv1805487	chr4:15760071-15768467	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv1810566	chr4:15760071-15768467	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv2421413	chr4:15760071-15768467	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv441859	chr4:15760071-15768467	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv436428	chr4:15760175-15768831	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv3464815	chr4:15760284-15768947	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv3464814	chr4:15760295-15768868	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv3464813	chr4:15760316-15768908	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv3464816	chr4:15760386-15768832	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	esv11795	chr4:15760451-15768822	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv516315	chr4:15760487-15767752	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
16	nsv1013204	chr4:15762970-15836237	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
17	nsv514199	chr4:15765852-15768377	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10002171	C1QTNF7	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15759200-15767800	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr4:15762000-15767800	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr4:15763000-15769800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:15764800-15775800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr4:15765600-15768000	Flanking Active TSS	Dnd41	blood
6	chr4:15766200-15767800	Enhancers	Fetal Thymus	thymus
7	chr4:15766200-15769000	Enhancers	Primary hematopoietic stem cells	blood
8	chr4:15766200-15769800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr4:15766400-15768200	Enhancers	Primary T cells from cord blood	blood
10	chr4:15766400-15769000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr4:15766800-15768800	Enhancers	Primary B cells from peripheral blood	blood
12	chr4:15766800-15770000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr4:15766800-15771000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr4:15766800-15771200	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr4:15767000-15769000	Enhancers	Primary B cells from cord blood	blood
16	chr4:15767000-15769000	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr4:15767000-15771200	Enhancers	Primary T cells fromperipheralblood	blood
18	chr4:15767200-15768000	Enhancers	Right Ventricle	heart
19	chr4:15767200-15768400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr4:15767200-15771000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr4:15767200-15771200	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr4:15767200-15771200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr4:15767200-15771200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr4:15767200-15779400	Weak transcription	Spleen	Spleen
25	chr4:15767400-15767800	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr4:15767400-15767800	Enhancers	Fetal Stomach	stomach
27	chr4:15767400-15768600	Enhancers	Liver	Liver
28	chr4:15767400-15769800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr4:15767600-15767800	Enhancers	Fetal Intestine Small	intestine
30	chr4:15767600-15767800	Flanking Active TSS	GM12878-XiMat	blood
31	chr4:15767600-15768000	Enhancers	Thymus	Thymus
32	chr4:15767600-15768200	Enhancers	Fetal Lung	lung
33	chr4:15767600-15768800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:15767600-15768800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr4:15767600-15769000	Enhancers	Duodenum Mucosa	Duodenum

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