Variant report

Variant	rs4841055
Chromosome Location	chr8:8699161-8699162
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10046783	0.81[CHB][hapmap]
rs10046784	0.81[CHB][hapmap]
rs1039916	1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs1115138	0.81[CHB][hapmap]
rs11249893	0.83[ASN][1000 genomes]
rs11783966	0.88[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap]
rs12547493	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs12677550	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[MEX][hapmap]
rs12682352	0.90[CHB][hapmap]
rs13254903	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13265731	0.88[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap]
rs1567398	0.91[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1876836	0.80[CHB][hapmap]
rs2428	0.90[CHB][hapmap]
rs332039	0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs332040	0.91[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs3789843	0.83[ASN][1000 genomes]
rs3827806	0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs408459	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs435953	0.86[ASN][1000 genomes]
rs437895	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4382480	0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs440788	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4481596	0.86[ASN][1000 genomes]
rs4841044	0.88[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap]
rs4841051	1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs4841054	0.82[EUR][1000 genomes]
rs6601265	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	0.92[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap]
rs6996376	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7006589	0.92[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap]
rs7017599	0.83[ASN][1000 genomes]
rs7813355	0.92[CEU][hapmap]
rs7820324	0.92[CEU][hapmap]
rs907183	0.91[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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
15	nsv1024055	chr8:8697249-8721016	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv539459	chr8:8697249-8721016	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4841055	TDH	cis	cerebellum	SCAN
rs4841055	CLDN23	cis	multi-tissue	Pritchard
rs4841055	C8orf13	cis	multi-tissue	Pritchard
rs4841055	PRSS55	cis	cerebellum	SCAN
rs4841055	FLJ10661	cis	cerebellum	SCAN
rs4841055	CTSB	cis	cerebellum	SCAN

Chromatin state (count:68 , 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	chr8:8675800-8699800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr8:8676200-8699400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr8:8678800-8701600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr8:8679600-8701400	Weak transcription	A549	lung
13	chr8:8679600-8701600	Weak transcription	HepG2	liver
14	chr8:8680400-8700200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr8:8681800-8700000	Weak transcription	Fetal Thymus	thymus
16	chr8:8683200-8701400	Weak transcription	Fetal Intestine Small	intestine
17	chr8:8683800-8701000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr8:8684200-8700800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr8:8684600-8703800	Weak transcription	Dnd41	blood
20	chr8:8686400-8700000	Weak transcription	Spleen	Spleen
21	chr8:8686400-8702000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr8:8686600-8705600	Weak transcription	Right Atrium	heart
23	chr8:8686800-8700000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr8:8686800-8702400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr8:8687000-8701400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr8:8687600-8706600	Weak transcription	Lung	lung
27	chr8:8692200-8701200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr8:8692200-8702000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr8:8692200-8717600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr8:8692400-8701000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr8:8692600-8701000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr8:8692600-8703200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr8:8692600-8707000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr8:8693600-8699200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr8:8693800-8700000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr8:8694200-8701600	Weak transcription	Small Intestine	intestine
37	chr8:8695000-8700000	Weak transcription	Gastric	stomach
38	chr8:8695000-8701400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr8:8695200-8701600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr8:8695400-8701400	Weak transcription	NHDF-Ad	bronchial
41	chr8:8695400-8701800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr8:8696000-8700400	Enhancers	Fetal Brain Male	brain
43	chr8:8696000-8701400	Weak transcription	K562	blood
44	chr8:8696400-8699200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr8:8697000-8699200	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr8:8697200-8699200	Weak transcription	Fetal Lung	lung
47	chr8:8697200-8704000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr8:8697600-8699600	Enhancers	Psoas Muscle	Psoas
49	chr8:8698200-8699200	Weak transcription	Brain Anterior Caudate	brain
50	chr8:8698200-8700400	Enhancers	Right Ventricle	heart

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