Variant report

Variant	rs907183
Chromosome Location	chr8:8729761-8729762
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:8729141..8730774-chr8:8738935..8740883,2	MCF-7	breast:
2	chr8:8728731..8732330-chr8:8733587..8735622,3	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1039915	0.93[CEU][hapmap]
rs1039916	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap]
rs11784052	0.82[CEU][hapmap];0.89[MEX][hapmap]
rs12544992	0.96[CEU][hapmap]
rs12547493	0.89[CEU][hapmap];0.89[MEX][hapmap];0.80[TSI][hapmap]
rs12677550	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs12679021	0.82[CHB][hapmap]
rs12682352	0.93[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.89[MEX][hapmap]
rs13254903	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs13259216	0.89[CEU][hapmap];0.89[MEX][hapmap]
rs1533058	0.89[CEU][hapmap];0.89[MEX][hapmap]
rs1533059	0.89[CEU][hapmap];0.89[MEX][hapmap]
rs1567398	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1821007	0.88[ASN][1000 genomes]
rs1876836	0.89[JPT][hapmap]
rs2428	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[MEX][hapmap]
rs332037	0.89[ASN][1000 genomes]
rs332039	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs332040	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789843	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3827806	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs408459	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs435953	0.81[ASN][1000 genomes]
rs437895	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs4382480	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs440788	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs4481596	0.81[EUR][1000 genomes]
rs4840362	0.82[CEU][hapmap];0.89[MEX][hapmap]
rs4841042	0.82[CEU][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs4841051	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap]
rs4841055	0.91[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4841058	0.82[CHB][hapmap]
rs6601265	0.82[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs6994038	0.81[CEU][hapmap]
rs7017599	0.97[ASN][1000 genomes]
rs7823757	0.80[CEU][hapmap]
rs7832968	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
8	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
9	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
10	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
11	esv2757257	chr8:8707639-8747894	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	esv2759591	chr8:8707639-8747894	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv818595	chr8:8712895-8752684	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv1030977	chr8:8725992-8739514	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv1026305	chr8:8726128-8739514	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs907183	CLDN23	cis	multi-tissue	Pritchard
rs907183	CTA-398F10.2	cis	Skin Sun Exposed Lower leg	GTEx
rs907183	PRSS55	cis	cerebellum	SCAN
rs907183	C8orf13	cis	multi-tissue	Pritchard
rs907183	SGK223	cis	Thyroid	GTEx
rs907183	TDH	cis	cerebellum	SCAN
rs907183	CTSB	cis	cerebellum	SCAN
rs907183	DEFB136	cis	parietal	SCAN
rs907183	FLJ10661	cis	cerebellum	SCAN
rs907183	MFHAS1	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8709600-8730000	Weak transcription	HSMMtube	muscle
2	chr8:8714400-8730000	Weak transcription	Aorta	Aorta
3	chr8:8714800-8730000	Weak transcription	Brain Angular Gyrus	brain
4	chr8:8717800-8735200	Weak transcription	Esophagus	oesophagus
5	chr8:8718000-8730000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr8:8718200-8729800	Weak transcription	Right Ventricle	heart
7	chr8:8718400-8742200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr8:8718600-8729800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr8:8718800-8730400	Weak transcription	HSMM	muscle
10	chr8:8719000-8730400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr8:8724600-8735000	Weak transcription	Brain Substantia Nigra	brain
12	chr8:8725200-8730000	Enhancers	Fetal Thymus	thymus
13	chr8:8725400-8730000	Enhancers	Fetal Brain Male	brain
14	chr8:8725800-8731000	Enhancers	Primary B cells from cord blood	blood
15	chr8:8725800-8732800	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr8:8726000-8730600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr8:8726000-8730600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr8:8726000-8731000	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr8:8726000-8731600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr8:8726000-8732200	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr8:8726000-8732200	Enhancers	Fetal Intestine Large	intestine
22	chr8:8726000-8732600	Enhancers	Duodenum Mucosa	Duodenum
23	chr8:8726200-8730000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr8:8726800-8729800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr8:8726800-8737600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr8:8726800-8737600	Weak transcription	NHEK	skin
27	chr8:8727000-8729800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr8:8727000-8730000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr8:8727000-8731200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr8:8727200-8729800	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr8:8727200-8729800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr8:8727200-8729800	Enhancers	Thymus	Thymus
33	chr8:8727200-8730600	Enhancers	Placenta	Placenta
34	chr8:8727200-8730800	Enhancers	Primary B cells from peripheral blood	blood
35	chr8:8727200-8732800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr8:8727400-8729800	Enhancers	Primary T cells fromperipheralblood	blood
37	chr8:8727400-8729800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr8:8727400-8732600	Enhancers	Stomach Mucosa	stomach
39	chr8:8727600-8729800	Enhancers	Primary T cells from cord blood	blood
40	chr8:8727600-8729800	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr8:8727600-8730000	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr8:8727600-8730000	Enhancers	Rectal Smooth Muscle	rectum
43	chr8:8727600-8730200	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr8:8727600-8731800	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr8:8727600-8733400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr8:8727800-8729800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr8:8727800-8730800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr8:8727800-8732800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr8:8727800-8733200	Enhancers	Liver	Liver
50	chr8:8728200-8730000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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