Variant report

Variant	rs9378688
Chromosome Location	chr6:2235633-2235634
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	chr6:2222298..2224652-chr6:2235622..2237446,2	MCF-7	breast:
2	chr6:2235011..2238207-chr6:2241335..2245707,5	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11242758	0.85[ASN][1000 genomes]
rs11961324	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11962550	0.82[ASN][1000 genomes]
rs11963138	1.00[ASN][1000 genomes]
rs11963529	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11965306	1.00[YRI][hapmap]
rs11970276	1.00[YRI][hapmap]
rs12191002	0.85[ASN][1000 genomes]
rs12661136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13196306	0.99[ASN][1000 genomes]
rs13217030	1.00[ASN][1000 genomes]
rs17134732	1.00[YRI][hapmap]
rs2295008	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2450299	0.96[ASN][1000 genomes]
rs2450304	1.00[ASN][1000 genomes]
rs2450307	0.96[ASN][1000 genomes]
rs2450310	0.87[ASN][1000 genomes]
rs2479001	0.96[ASN][1000 genomes]
rs2479002	0.96[ASN][1000 genomes]
rs2479004	0.96[ASN][1000 genomes]
rs2479008	0.87[ASN][1000 genomes]
rs2479011	0.85[ASN][1000 genomes]
rs2479014	0.85[ASN][1000 genomes]
rs2505657	0.89[ASN][1000 genomes]
rs2505658	0.89[ASN][1000 genomes]
rs2505659	0.96[ASN][1000 genomes]
rs2505660	0.96[ASN][1000 genomes]
rs2505661	0.96[ASN][1000 genomes]
rs2505662	0.93[ASN][1000 genomes]
rs2505663	0.96[ASN][1000 genomes]
rs2505666	0.96[ASN][1000 genomes]
rs2505667	0.98[ASN][1000 genomes]
rs2505670	0.83[ASN][1000 genomes]
rs2505671	0.85[ASN][1000 genomes]
rs2505673	0.85[ASN][1000 genomes]
rs2505677	0.89[ASN][1000 genomes]
rs2505678	0.89[ASN][1000 genomes]
rs36016883	0.84[ASN][1000 genomes]
rs3778557	1.00[YRI][hapmap]
rs3778568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3800184	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3800185	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3800187	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3800190	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3823287	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55992523	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56196406	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6596879	0.85[ASN][1000 genomes]
rs72830182	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72830184	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7754950	1.00[ASN][1000 genomes]
rs9328087	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs9378327	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9378684	1.00[YRI][hapmap]
rs9378685	1.00[YRI][hapmap]
rs9378686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9378687	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9378692	0.98[ASN][1000 genomes]
rs9378693	0.98[ASN][1000 genomes]
rs9391946	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs9392371	1.00[YRI][hapmap]
rs9392373	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9392374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9392375	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9392377	1.00[ASN][1000 genomes]
rs9405550	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
4	nsv1025814	chr6:2064629-2308518	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv538098	chr6:2064629-2308518	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv1030181	chr6:2071210-2308657	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv538099	chr6:2071210-2308657	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
9	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
10	nsv830573	chr6:2120985-2263646	Bivalent Enhancer Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
11	nsv1022623	chr6:2199666-2267750	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
12	nsv538100	chr6:2199666-2267750	ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	nsv1022166	chr6:2199666-2320800	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
14	nsv1017174	chr6:2213893-2340529	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
15	nsv1033201	chr6:2218647-2308518	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
16	nsv538101	chr6:2218647-2308518	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
17	nsv1026678	chr6:2230064-2261297	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	n/a
18	esv2763526	chr6:2230064-2311916	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Caudate nucleus volume	21502949	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9378688	WRNIP1	cis	parietal	SCAN
rs9378688	LYRM4	cis	parietal	SCAN
rs9378688	C6orf145	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2222600-2244400	Weak transcription	Fetal Stomach	stomach
2	chr6:2222600-2244600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:2222800-2243800	Weak transcription	Primary T cells from cord blood	blood
4	chr6:2227200-2236200	Weak transcription	Hela-S3	cervix
5	chr6:2227800-2239800	Weak transcription	Fetal Intestine Small	intestine
6	chr6:2228200-2236400	Weak transcription	Pancreas	Pancrea
7	chr6:2228600-2243800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:2231600-2243200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:2231600-2243800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:2231800-2236400	Weak transcription	NHLF	lung
11	chr6:2231800-2237600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:2231800-2238200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:2231800-2242600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:2231800-2244200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:2232000-2236200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:2232000-2236400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:2232000-2236400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr6:2232000-2236600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:2232000-2236800	Weak transcription	HUVEC	blood vessel
20	chr6:2232000-2237200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:2232000-2237400	Weak transcription	HSMM	muscle
22	chr6:2232000-2237600	Weak transcription	NH-A	brain
23	chr6:2232000-2244800	Weak transcription	Aorta	Aorta
24	chr6:2232200-2236400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:2232200-2236600	Weak transcription	NHDF-Ad	bronchial
26	chr6:2232200-2237000	Weak transcription	NHEK	skin
27	chr6:2232200-2237200	Weak transcription	HMEC	breast
28	chr6:2232400-2237000	Genic enhancers	HepG2	liver
29	chr6:2232600-2236600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:2233000-2236400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:2233000-2240200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr6:2233200-2236400	Weak transcription	Gastric	stomach
33	chr6:2233200-2239800	Weak transcription	Small Intestine	intestine
34	chr6:2233200-2241200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr6:2233200-2244000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:2233400-2244400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr6:2233400-2244400	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr6:2233400-2244600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr6:2233600-2236200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:2233600-2236400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr6:2233600-2236400	Weak transcription	Osteobl	bone
42	chr6:2233600-2241000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr6:2233800-2241000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr6:2234200-2235800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:2234200-2241000	Weak transcription	GM12878-XiMat	blood
46	chr6:2235200-2238400	Enhancers	Stomach Mucosa	stomach
47	chr6:2235600-2237000	Enhancers	Fetal Brain Female	brain

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