Variant report

Variant	rs4413788
Chromosome Location	chr8:19336762-19336763
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:19335994..19338112-chr8:19352169..19353852,2	K562	blood:

Variant related genes	Relation type
ENSG00000147408	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10088454	0.87[CHD][hapmap]
rs10089231	0.87[CHD][hapmap]
rs10101192	0.87[CHD][hapmap]
rs10105097	0.80[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10105363	0.83[CHD][hapmap]
rs10107348	0.89[CHB][hapmap]
rs10109274	0.87[CHD][hapmap]
rs10503653	0.83[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs10888165	0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11204044	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11204045	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204046	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11204047	1.00[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11204048	0.89[ASN][1000 genomes]
rs11204049	0.91[ASN][1000 genomes]
rs11204050	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11777566	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11778734	0.94[CEU][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11780475	0.80[ASN][1000 genomes]
rs11783263	1.00[JPT][hapmap]
rs12682196	0.89[JPT][hapmap]
rs13250181	0.89[JPT][hapmap]
rs13261442	1.00[JPT][hapmap]
rs13261732	0.89[JPT][hapmap]
rs13265751	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13266857	0.80[CHD][hapmap];1.00[JPT][hapmap]
rs13267265	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13267569	0.96[ASN][1000 genomes]
rs13276417	1.00[JPT][hapmap]
rs13278459	0.89[CHB][hapmap]
rs13280711	0.80[ASN][1000 genomes]
rs13282951	0.87[CHD][hapmap]
rs17128525	0.80[CHD][hapmap];1.00[JPT][hapmap]
rs17128556	0.87[CHD][hapmap]
rs17128604	0.83[CHD][hapmap]
rs17479777	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs28490401	0.83[CHD][hapmap]
rs3185	0.89[JPT][hapmap]
rs3923920	0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4073790	0.80[ASN][1000 genomes]
rs4073791	0.80[ASN][1000 genomes]
rs4244451	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4244452	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4244453	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4292704	0.89[JPT][hapmap]
rs4311666	0.94[CEU][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4317590	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4319111	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs4339658	0.80[ASN][1000 genomes]
rs4442162	0.86[EUR][1000 genomes]
rs4442163	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4455848	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4472532	0.87[CHD][hapmap]
rs4483172	0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4484715	0.80[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4513991	0.91[ASN][1000 genomes]
rs4524812	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4540423	0.84[EUR][1000 genomes]
rs4554481	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs4599829	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4614013	0.91[ASN][1000 genomes]
rs4631482	0.92[ASN][1000 genomes]
rs4631483	0.82[ASN][1000 genomes]
rs4921646	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4921647	0.94[CEU][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4921648	1.00[CEU][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4921649	1.00[CEU][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4921651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4921652	0.93[ASN][1000 genomes]
rs4921653	0.80[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4921654	0.80[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4921656	1.00[JPT][hapmap]
rs4921657	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4922034	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4922036	0.89[JPT][hapmap]
rs4922037	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4922038	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4922039	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4922041	0.91[ASN][1000 genomes]
rs4922044	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4922045	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4922046	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4922047	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4922048	0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4922049	0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs5013219	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6586836	0.86[ASN][1000 genomes]
rs6586837	1.00[CEU][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6586838	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6586839	1.00[JPT][hapmap]
rs6586840	1.00[JPT][hapmap]
rs6984449	0.89[JPT][hapmap]
rs6984644	0.80[CHD][hapmap];1.00[JPT][hapmap]
rs6988743	0.80[ASN][1000 genomes]
rs6991941	1.00[JPT][hapmap]
rs6994352	0.94[CEU][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6998334	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6998991	0.87[ASN][1000 genomes]
rs6999542	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7002357	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7002643	0.83[CHD][hapmap]
rs7005075	1.00[JPT][hapmap]
rs7017776	1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7460541	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7464357	0.92[ASN][1000 genomes]
rs7464358	0.92[ASN][1000 genomes]
rs7814548	0.87[CHD][hapmap]
rs7816777	1.00[JPT][hapmap]
rs7818691	0.90[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs7828197	0.80[ASN][1000 genomes]
rs7830404	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7839041	0.94[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9644628	0.80[ASN][1000 genomes]
rs9644629	0.80[ASN][1000 genomes]
rs9644631	0.85[CHD][hapmap];1.00[JPT][hapmap];0.80[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	nsv1015395	chr8:18489538-19370258	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv429907	chr8:18578720-19398220	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv949745	chr8:18826830-19363963	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1016482	chr8:18834807-19339487	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer 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
5	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
6	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
7	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
8	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
9	esv3693374	chr8:19241970-19359184	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
10	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
11	nsv890623	chr8:19307051-19383697	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4413788	CSGALNACT1	cis	cerebellum	SCAN
rs4413788	CSGALNACT1	cis	parietal	SCAN
rs4413788	FAM160B2	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19310600-19359600	Weak transcription	Ovary	ovary
2	chr8:19316200-19339200	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr8:19319600-19362800	Weak transcription	Spleen	Spleen
4	chr8:19328000-19337800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr8:19330000-19338200	Weak transcription	Placenta	Placenta
6	chr8:19331000-19352800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr8:19333000-19337000	Enhancers	NHDF-Ad	bronchial
8	chr8:19333000-19339400	Enhancers	Primary T cells from cord blood	blood
9	chr8:19333200-19338200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr8:19333200-19338400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr8:19333400-19362200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr8:19334200-19339200	Weak transcription	Fetal Thymus	thymus
13	chr8:19334400-19339400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr8:19334600-19347400	Weak transcription	Right Atrium	heart
15	chr8:19334800-19337600	Weak transcription	Left Ventricle	heart
16	chr8:19334800-19338600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr8:19335000-19338000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr8:19335000-19338000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr8:19335000-19338200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr8:19335000-19338200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr8:19335000-19338200	Weak transcription	Aorta	Aorta
22	chr8:19335000-19338200	Weak transcription	Hela-S3	cervix
23	chr8:19335000-19338200	Weak transcription	HSMMtube	muscle
24	chr8:19335000-19338200	Weak transcription	Osteobl	bone
25	chr8:19335000-19338400	Weak transcription	HSMM	muscle
26	chr8:19335000-19339400	Weak transcription	Right Ventricle	heart
27	chr8:19335400-19339200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr8:19335800-19339000	Strong transcription	Primary B cells from cord blood	blood
29	chr8:19336000-19336800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr8:19336000-19336800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr8:19336000-19337200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr8:19336000-19341800	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr8:19336000-19341800	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr8:19336000-19345000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr8:19336200-19337400	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr8:19336200-19338000	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr8:19336200-19338200	Weak transcription	A549	lung
38	chr8:19336400-19336800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr8:19336400-19336800	Enhancers	NHLF	lung
40	chr8:19336400-19337600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr8:19336400-19338000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr8:19336600-19337000	Enhancers	Primary T cells fromperipheralblood	blood
43	chr8:19336600-19337000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr8:19336600-19338000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr8:19336600-19340200	Enhancers	Primary T killer memory cells from peripheral blood	blood

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