Variant report

Variant	rs11204046
Chromosome Location	chr8:19342557-19342558
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 133 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10088454	0.82[CHD][hapmap]
rs10089231	0.82[CHD][hapmap]
rs10101192	0.82[CHD][hapmap]
rs10105097	0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10107348	0.89[CHB][hapmap]
rs10109274	0.82[CHD][hapmap]
rs1013438	1.00[CEU][hapmap]
rs10503653	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs10888165	0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11204044	0.80[ASN][1000 genomes]
rs11204045	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11204047	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204048	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204049	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204050	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11204052	0.85[ASN][1000 genomes]
rs11777566	0.84[ASN][1000 genomes]
rs11778734	0.82[CEU][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs11780475	0.86[ASN][1000 genomes]
rs11783263	0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12682196	0.89[JPT][hapmap]
rs13250181	0.89[JPT][hapmap]
rs13261442	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13261732	0.89[JPT][hapmap]
rs13265751	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs13266857	0.84[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13267265	0.95[ASN][1000 genomes]
rs13267569	0.95[ASN][1000 genomes]
rs13276417	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13278459	0.89[CHB][hapmap]
rs13280711	0.86[ASN][1000 genomes]
rs13282951	0.82[CHD][hapmap]
rs17128525	0.84[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17128556	0.82[CHD][hapmap]
rs17479777	0.80[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28671342	0.85[ASN][1000 genomes]
rs2958576	1.00[CEU][hapmap]
rs3185	0.89[JPT][hapmap]
rs3923920	0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4073790	0.86[ASN][1000 genomes]
rs4073791	0.86[ASN][1000 genomes]
rs4244451	0.83[ASN][1000 genomes]
rs4244452	0.84[ASN][1000 genomes]
rs4244453	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4244454	0.93[CEU][hapmap];0.83[TSI][hapmap]
rs4273861	0.83[ASN][1000 genomes]
rs4292704	0.89[JPT][hapmap]
rs4311666	0.82[CEU][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4317590	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4319111	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4339658	0.86[ASN][1000 genomes]
rs4410924	1.00[CEU][hapmap]
rs4413788	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4442163	0.93[ASN][1000 genomes]
rs4455848	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4472532	0.82[CHD][hapmap]
rs4483172	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4484715	0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4513991	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4524812	0.84[ASN][1000 genomes]
rs4554481	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4599829	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4614013	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4631482	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4631483	0.85[ASN][1000 genomes]
rs4921646	0.84[ASN][1000 genomes]
rs4921647	0.82[CEU][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4921648	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4921649	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4921651	0.86[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.81[TSI][hapmap];0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4921652	0.95[ASN][1000 genomes]
rs4921653	0.84[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4921654	0.84[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4921655	0.85[ASN][1000 genomes]
rs4921656	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4921657	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4922034	0.83[ASN][1000 genomes]
rs4922036	0.89[JPT][hapmap]
rs4922037	0.91[ASN][1000 genomes]
rs4922038	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4922039	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4922041	0.87[CEU][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4922044	0.80[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4922045	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4922046	0.87[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4922047	0.87[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4922048	0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4922049	0.80[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4922065	1.00[CEU][hapmap];0.84[TSI][hapmap]
rs5013219	0.84[ASN][1000 genomes]
rs6586836	0.83[ASN][1000 genomes]
rs6586837	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs6586838	0.83[ASN][1000 genomes]
rs6586839	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6586840	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6586843	1.00[CEU][hapmap]
rs6984449	0.89[JPT][hapmap]
rs6984644	0.84[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6988743	0.86[ASN][1000 genomes]
rs6991941	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6994352	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs6998334	0.87[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6998991	0.93[ASN][1000 genomes]
rs6999542	0.80[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7005075	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7017776	0.87[CEU][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73585587	0.80[ASN][1000 genomes]
rs7460541	0.93[ASN][1000 genomes]
rs7464357	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7464358	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7814548	0.82[CHD][hapmap]
rs7816777	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7818691	0.90[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs7828197	0.84[ASN][1000 genomes]
rs7830404	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7838412	1.00[CEU][hapmap]
rs7839041	0.82[CEU][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs7841402	0.93[CEU][hapmap]
rs9644628	0.86[ASN][1000 genomes]
rs9644629	0.86[ASN][1000 genomes]
rs9644630	0.84[ASN][1000 genomes]
rs9644631	0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
rs11204046	CSGALNACT1	cis	parietal	SCAN
rs11204046	CSGALNACT1	cis	cerebellum	SCAN
rs11204046	PDGFRL	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19310600-19359600	Weak transcription	Ovary	ovary
2	chr8:19319600-19362800	Weak transcription	Spleen	Spleen
3	chr8:19331000-19352800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr8:19333400-19362200	Weak transcription	Primary B cells from peripheral blood	blood
5	chr8:19334600-19347400	Weak transcription	Right Atrium	heart
6	chr8:19336000-19345000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr8:19337600-19342600	Enhancers	Left Ventricle	heart
8	chr8:19338000-19351000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr8:19338600-19344000	Weak transcription	Brain Anterior Caudate	brain
10	chr8:19338800-19347200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr8:19338800-19370600	Weak transcription	Esophagus	oesophagus
12	chr8:19339000-19347800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr8:19339000-19351800	Weak transcription	Primary B cells from cord blood	blood
14	chr8:19339400-19352800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr8:19339800-19343400	Weak transcription	Thymus	Thymus
16	chr8:19340000-19348400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr8:19340000-19352800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr8:19340200-19343400	Weak transcription	Fetal Thymus	thymus
19	chr8:19341000-19343200	Genic enhancers	A549	lung
20	chr8:19341000-19347200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr8:19341200-19343400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr8:19341200-19347600	Weak transcription	Placenta	Placenta
23	chr8:19341200-19351000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr8:19341400-19343000	Weak transcription	Primary T cells from cord blood	blood
25	chr8:19341400-19347000	Weak transcription	Brain Angular Gyrus	brain
26	chr8:19341400-19354200	Weak transcription	Brain Substantia Nigra	brain
27	chr8:19341600-19344000	Enhancers	Hela-S3	cervix
28	chr8:19341600-19347400	Weak transcription	Right Ventricle	heart
29	chr8:19341800-19342800	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr8:19341800-19343000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr8:19341800-19344400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr8:19341800-19351600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr8:19342200-19345600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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