Variant report

Variant	rs6996732
Chromosome Location	chr8:19418028-19418029
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10096224	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10100589	0.83[CHD][hapmap]
rs10106622	0.83[CHD][hapmap]
rs10282938	0.93[CEU][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.93[MEX][hapmap]
rs10282948	0.93[CEU][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes]
rs10283186	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11988176	0.93[CEU][hapmap]
rs11988991	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11995671	0.83[CHD][hapmap]
rs11996428	0.83[CHD][hapmap]
rs12334858	0.93[CEU][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs13260841	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13263246	0.83[CHD][hapmap]
rs34362100	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35265506	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4332151	0.93[CEU][hapmap]
rs4507779	0.93[CEU][hapmap]
rs4549790	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4563899	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4922059	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4922062	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55808915	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6586847	1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs6586848	0.93[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs6986805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6995903	0.83[CHD][hapmap]
rs6998022	0.93[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes];0.91[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	nsv533109	chr8:18845845-19456780	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	20 gene(s)	inside rSNPs	diseases
2	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv948861	chr8:19199688-19609029	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv949304	chr8:19199688-19625912	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer 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	11 gene(s)	inside rSNPs	diseases
5	esv34007	chr8:19252602-19482098	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv890624	chr8:19319061-19456270	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv610753	chr8:19364883-19439977	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv890625	chr8:19368697-19799641	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1018057	chr8:19370830-19435399	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1016276	chr8:19374998-19435147	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv890626	chr8:19383697-19483259	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv890627	chr8:19389865-19561997	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6996732	ZDHHC2	cis	cerebellum	SCAN
rs6996732	TNFRSF10C	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19379400-19434200	Weak transcription	Placenta	Placenta
2	chr8:19401400-19434000	Weak transcription	Hela-S3	cervix
3	chr8:19409000-19437400	Weak transcription	Gastric	stomach
4	chr8:19413800-19418200	Weak transcription	Right Atrium	heart
5	chr8:19415200-19418200	Weak transcription	Right Ventricle	heart
6	chr8:19415200-19419000	Weak transcription	Fetal Thymus	thymus
7	chr8:19415200-19419000	Weak transcription	Left Ventricle	heart
8	chr8:19415200-19422400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr8:19415400-19424400	Weak transcription	Aorta	Aorta
10	chr8:19415800-19419000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr8:19416600-19419000	Weak transcription	Brain Anterior Caudate	brain
12	chr8:19417000-19418400	Genic enhancers	A549	lung
13	chr8:19417000-19418800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr8:19417000-19419200	Weak transcription	Brain Angular Gyrus	brain
15	chr8:19417000-19420000	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr8:19417000-19420000	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr8:19417000-19420400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr8:19417200-19421200	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr8:19417400-19419000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr8:19417400-19419600	Enhancers	Primary T cells from cord blood	blood
21	chr8:19417400-19420000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr8:19417600-19419800	Enhancers	Primary B cells from cord blood	blood
23	chr8:19417600-19419800	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr8:19417800-19418400	Enhancers	Primary hematopoietic stem cells	blood
25	chr8:19417800-19418400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr8:19418000-19418200	Enhancers	Fetal Heart	heart
27	chr8:19418000-19418400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr8:19418000-19418400	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr8:19418000-19418400	Enhancers	Primary B cells from peripheral blood	blood
30	chr8:19418000-19418400	Enhancers	Primary T cells fromperipheralblood	blood
31	chr8:19418000-19418400	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr8:19418000-19418400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr8:19418000-19418400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr8:19418000-19418400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr8:19418000-19418400	Enhancers	Thymus	Thymus
36	chr8:19418000-19418400	Enhancers	Spleen	Spleen
37	chr8:19418000-19418400	Enhancers	Dnd41	blood
38	chr8:19418000-19418400	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr8:19418000-19418600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr8:19418000-19418600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr8:19418000-19419200	Enhancers	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links