Variant report

Variant	rs6601265
Chromosome Location	chr8:8695574-8695575
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1039916	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs11249893	0.87[ASN][1000 genomes]
rs11783966	0.84[CEU][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap]
rs11995244	0.82[CHB][hapmap]
rs12547493	0.83[JPT][hapmap]
rs12677550	0.92[CEU][hapmap];0.82[CHB][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs12682352	0.82[CHB][hapmap]
rs13254903	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13265731	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs1510932	0.81[CHB][hapmap]
rs1567398	0.82[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs2428	0.82[CHB][hapmap]
rs332039	0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs332040	0.82[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs35654766	0.84[EUR][1000 genomes]
rs3827806	0.82[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs408459	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs435953	0.85[AMR][1000 genomes]
rs437895	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4382480	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs440788	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4840365	0.82[EUR][1000 genomes]
rs4841044	0.84[CEU][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap]
rs4841051	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs4841054	0.87[EUR][1000 genomes]
rs4841055	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6993494	0.88[CEU][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap]
rs6996376	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7006589	0.88[CEU][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap]
rs7813355	0.88[CEU][hapmap];0.87[GIH][hapmap];0.82[EUR][1000 genomes]
rs7820324	0.96[CEU][hapmap];0.90[GIH][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs907183	0.82[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs9329169	0.82[CHB][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	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1019606	chr8:8353661-8736992	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv539456	chr8:8353661-8736992	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv995047	chr8:8353662-8857913	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1022511	chr8:8493992-8737132	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv539457	chr8:8493992-8737132	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	esv1824870	chr8:8583943-8699382	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	nsv831228	chr8:8608387-8790790	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv1018828	chr8:8609880-8790660	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv1022331	chr8:8610035-8787981	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
12	nsv890338	chr8:8669622-8707970	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1015437	chr8:8681255-8723798	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv1023221	chr8:8695393-8722418	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6601265	CTSB	cis	cerebellum	SCAN
rs6601265	FLJ10661	cis	cerebellum	SCAN
rs6601265	PRSS55	cis	cerebellum	SCAN
rs6601265	TDH	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8667200-8699200	Weak transcription	Aorta	Aorta
2	chr8:8667200-8701600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr8:8667600-8701000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr8:8670000-8701200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr8:8670200-8701200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr8:8670400-8705400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr8:8672000-8700200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr8:8674800-8701800	Weak transcription	Primary T cells from cord blood	blood
9	chr8:8675200-8699000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr8:8675800-8699800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr8:8676200-8699400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr8:8678800-8701600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr8:8679600-8701400	Weak transcription	A549	lung
14	chr8:8679600-8701600	Weak transcription	HepG2	liver
15	chr8:8680400-8700200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr8:8681800-8700000	Weak transcription	Fetal Thymus	thymus
17	chr8:8683200-8701400	Weak transcription	Fetal Intestine Small	intestine
18	chr8:8683800-8701000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr8:8684200-8700800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr8:8684600-8703800	Weak transcription	Dnd41	blood
21	chr8:8686400-8700000	Weak transcription	Spleen	Spleen
22	chr8:8686400-8702000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr8:8686600-8705600	Weak transcription	Right Atrium	heart
24	chr8:8686800-8700000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr8:8686800-8702400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr8:8687000-8701400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr8:8687400-8696000	Weak transcription	Fetal Brain Male	brain
28	chr8:8687600-8698600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr8:8687600-8706600	Weak transcription	Lung	lung
30	chr8:8687800-8698200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr8:8688600-8698200	Weak transcription	Right Ventricle	heart
32	chr8:8689000-8698200	Weak transcription	Colon Smooth Muscle	Colon
33	chr8:8692200-8695600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr8:8692200-8698000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr8:8692200-8701200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr8:8692200-8702000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr8:8692200-8717600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr8:8692400-8701000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr8:8692600-8701000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr8:8692600-8703200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr8:8692600-8707000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr8:8693600-8699200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr8:8693800-8700000	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr8:8694200-8698600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr8:8694200-8701600	Weak transcription	Small Intestine	intestine
46	chr8:8694400-8695600	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr8:8695000-8696200	Enhancers	Fetal Lung	lung
48	chr8:8695000-8698800	Weak transcription	Left Ventricle	heart
49	chr8:8695000-8700000	Weak transcription	Gastric	stomach
50	chr8:8695000-8701400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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