Variant report

Variant	rs3802328
Chromosome Location	chr8:19297051-19297052
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:19291426..19297066-chr8:19613560..19616648,5	MCF-7	breast:
2	chr8:19277783..19279475-chr8:19295550..19297142,2	MCF-7	breast:
3	chr8:19271639..19274356-chr8:19296369..19298218,2	MCF-7	breast:
4	chr8:19275219..19277107-chr8:19294224..19297306,3	MCF-7	breast:
5	chr8:19294799..19297740-chr8:19300863..19302648,2	MCF-7	breast:
6	chr8:19280974..19282712-chr8:19296114..19297888,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147408	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10107348	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs10107416	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10481426	0.85[CHD][hapmap]
rs11204039	1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs11204040	0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11204041	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs11778175	0.82[CHD][hapmap]
rs11780343	1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[ASN][1000 genomes]
rs11784873	0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs11785649	0.89[CHD][hapmap]
rs11787230	0.91[CHB][hapmap];0.96[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs11991105	1.00[CHB][hapmap];0.83[YRI][hapmap];0.92[ASN][1000 genomes]
rs12542575	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12543061	0.91[CHB][hapmap];0.89[CHD][hapmap];0.89[ASN][1000 genomes]
rs12674938	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12675717	0.91[CHB][hapmap];0.92[ASN][1000 genomes]
rs12677088	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]
rs12678336	0.87[ASN][1000 genomes]
rs12679712	0.89[CHD][hapmap]
rs13255677	0.83[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13255946	0.89[CHD][hapmap]
rs13258090	0.83[CHB][hapmap];0.89[CHD][hapmap];0.88[ASN][1000 genomes]
rs13278459	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34156560	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35029660	0.83[ASN][1000 genomes]
rs4307360	0.81[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.83[YRI][hapmap];0.89[ASN][1000 genomes]
rs4333618	0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs4379462	0.86[JPT][hapmap]
rs4392915	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4392916	0.83[ASN][1000 genomes]
rs4409408	0.86[JPT][hapmap]
rs4412390	0.86[CHD][hapmap]
rs4430112	0.97[ASN][1000 genomes]
rs4433156	0.90[CHB][hapmap];0.88[ASN][1000 genomes]
rs4481612	0.91[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs4541947	0.85[JPT][hapmap]
rs4546679	0.88[ASN][1000 genomes]
rs4549789	0.88[ASN][1000 genomes]
rs4554480	0.88[ASN][1000 genomes]
rs4618712	0.91[ASN][1000 genomes]
rs4921638	0.89[CHD][hapmap]
rs4921642	0.97[ASN][1000 genomes]
rs4921643	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4921644	0.84[ASN][1000 genomes]
rs4921645	0.89[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4922028	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4922029	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs56298301	0.88[ASN][1000 genomes]
rs6586830	0.81[CHD][hapmap];0.91[MEX][hapmap]
rs6586833	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6981898	0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6983973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6984145	0.97[ASN][1000 genomes]
rs6990357	0.89[CHD][hapmap]
rs6992893	0.83[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6997164	0.97[ASN][1000 genomes]
rs6999786	0.89[CHD][hapmap]
rs7004435	0.88[ASN][1000 genomes]
rs7008916	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7011602	0.80[ASN][1000 genomes]
rs7012529	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7814793	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7818345	0.87[ASN][1000 genomes]
rs7820698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7821446	0.89[CHD][hapmap]
rs7822046	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7823194	0.97[ASN][1000 genomes]
rs7830251	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7833166	0.91[ASN][1000 genomes]
rs7835461	0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7835945	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7844175	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9720249	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3802328	INTS10	cis	parietal	SCAN
rs3802328	CSGALNACT1	cis	cerebellum	SCAN
rs3802328	CSGALNACT1	cis	parietal	SCAN
rs3802328	PHYHIP	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19271800-19305200	Weak transcription	Pancreas	Pancrea
2	chr8:19277600-19307800	Weak transcription	Fetal Stomach	stomach
3	chr8:19277800-19300200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr8:19278000-19304800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr8:19283800-19302200	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr8:19283800-19307800	Weak transcription	Ovary	ovary
7	chr8:19284000-19302400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr8:19284200-19300000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr8:19290400-19297600	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr8:19291200-19297600	Strong transcription	Primary B cells from cord blood	blood
11	chr8:19291600-19308000	Weak transcription	Right Ventricle	heart
12	chr8:19292600-19301400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr8:19294000-19297400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr8:19294400-19297400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr8:19294400-19297400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr8:19294400-19297600	Strong transcription	Primary T cells from cord blood	blood
17	chr8:19294600-19297200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr8:19294600-19297400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr8:19294600-19297600	Enhancers	H9 Cell Line	embryonic stem cell
20	chr8:19294600-19297600	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr8:19294600-19297600	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr8:19294600-19297600	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr8:19294600-19297600	Transcr. at gene 5' and 3'	A549	lung
24	chr8:19294600-19297800	Strong transcription	Placenta	Placenta
25	chr8:19294600-19302000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr8:19294800-19297200	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr8:19294800-19297600	Enhancers	H1 Cell Line	embryonic stem cell
28	chr8:19294800-19297600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr8:19294800-19297600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr8:19294800-19297600	Strong transcription	Left Ventricle	heart
31	chr8:19295000-19318800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr8:19295200-19297600	Enhancers	HSMMtube	muscle
33	chr8:19295400-19297200	Enhancers	HSMM	muscle
34	chr8:19295800-19302800	Weak transcription	Thymus	Thymus
35	chr8:19296000-19297400	Weak transcription	Spleen	Spleen
36	chr8:19296000-19297600	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr8:19296400-19297600	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr8:19296400-19297600	Enhancers	Brain Hippocampus Middle	brain
39	chr8:19296600-19302000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr8:19296600-19302000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr8:19296600-19302200	Weak transcription	HepG2	liver
42	chr8:19296600-19309400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr8:19296600-19317400	Weak transcription	Hela-S3	cervix
44	chr8:19296800-19297200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr8:19296800-19297200	Enhancers	Lung	lung
46	chr8:19296800-19297600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr8:19296800-19297600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr8:19296800-19300400	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr8:19297000-19297200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr8:19297000-19297200	Enhancers	Brain Substantia Nigra	brain

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