Variant report

Variant	rs12677088
Chromosome Location	chr8:19309945-19309946
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10107348	0.85[JPT][hapmap]
rs10107416	1.00[JPT][hapmap]
rs11204039	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs11204040	1.00[JPT][hapmap]
rs11204041	0.81[CHB][hapmap]
rs11780343	0.81[CHB][hapmap]
rs11784873	0.85[JPT][hapmap]
rs11787230	0.85[JPT][hapmap]
rs11991105	0.81[CHB][hapmap]
rs12542575	1.00[JPT][hapmap]
rs12674938	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs13255677	1.00[JPT][hapmap]
rs13278459	1.00[JPT][hapmap]
rs35029660	0.91[ASN][1000 genomes]
rs3802328	0.83[ASW][hapmap];0.95[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes]
rs4307360	1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[ASN][1000 genomes]
rs4333618	0.85[JPT][hapmap]
rs4379462	0.86[JPT][hapmap]
rs4392915	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4392916	0.91[ASN][1000 genomes]
rs4409408	0.86[JPT][hapmap]
rs4481612	0.85[JPT][hapmap]
rs4541947	0.85[JPT][hapmap]
rs4618712	0.83[ASN][1000 genomes]
rs4921643	0.95[CEU][hapmap]
rs4921645	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4922028	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4922029	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs56298301	0.85[ASN][1000 genomes]
rs6586830	0.91[MEX][hapmap]
rs6586833	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6981898	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6983973	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs6992893	1.00[JPT][hapmap]
rs7011602	0.88[ASN][1000 genomes]
rs7814793	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7818345	0.84[ASN][1000 genomes]
rs7820698	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs7822046	0.95[CEU][hapmap];0.97[GIH][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap]
rs7830251	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7835461	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7835945	0.95[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv1016993	chr8:18855623-19311731	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	nsv610752	chr8:19254816-19311496	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
13	nsv1022344	chr8:19270143-19324083	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12677088	INTS10	cis	parietal	SCAN
rs12677088	PHYHIP	cis	parietal	SCAN
rs12677088	CSGALNACT1	cis	cerebellum	SCAN
rs12677088	CSGALNACT1	cis	brain	BrainEAC
rs12677088	CSGALNACT1	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19295000-19318800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:19296600-19317400	Weak transcription	Hela-S3	cervix
3	chr8:19297400-19313400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr8:19297600-19319000	Weak transcription	Spleen	Spleen
5	chr8:19300000-19313800	Weak transcription	Fetal Heart	heart
6	chr8:19300600-19319200	Weak transcription	Gastric	stomach
7	chr8:19301600-19317200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr8:19302800-19317800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr8:19303200-19313800	Weak transcription	HUVEC	blood vessel
10	chr8:19303400-19315200	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr8:19304200-19310200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr8:19305600-19313200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr8:19305600-19317600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr8:19305600-19318400	Weak transcription	Pancreas	Pancrea
15	chr8:19305800-19313000	Weak transcription	Placenta	Placenta
16	chr8:19306400-19312000	Enhancers	Primary T cells from cord blood	blood
17	chr8:19306600-19312000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr8:19306800-19311800	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr8:19306800-19322400	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr8:19307000-19310000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr8:19307800-19312000	Enhancers	Primary T cells fromperipheralblood	blood
22	chr8:19307800-19312000	Enhancers	Dnd41	blood
23	chr8:19308000-19313000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr8:19308000-19313000	Weak transcription	Fetal Kidney	kidney
25	chr8:19308200-19310200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr8:19308200-19310200	Weak transcription	Right Atrium	heart
27	chr8:19308200-19313000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr8:19308200-19313800	Weak transcription	Adipose Nuclei	Adipose
29	chr8:19308200-19317000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr8:19308200-19317000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr8:19308200-19317400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr8:19308200-19319000	Weak transcription	Lung	lung
33	chr8:19308400-19311000	Weak transcription	Thymus	Thymus
34	chr8:19308400-19313200	Weak transcription	Left Ventricle	heart
35	chr8:19308400-19313200	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr8:19308400-19317200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr8:19308400-19318200	Weak transcription	Right Ventricle	heart
38	chr8:19308800-19310000	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr8:19309000-19310400	Enhancers	H1 Cell Line	embryonic stem cell
40	chr8:19309000-19310400	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr8:19309000-19310600	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr8:19309200-19310000	Enhancers	Brain Angular Gyrus	brain
43	chr8:19309200-19310200	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr8:19309400-19310200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr8:19309400-19310400	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr8:19309400-19310400	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr8:19309400-19310600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr8:19309400-19310600	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr8:19309400-19311000	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr8:19309400-19311000	Enhancers	Fetal Brain Male	brain

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