Variant report

Variant	rs9959061
Chromosome Location	chr18:12870038-12870039
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12857931..12860892-chr18:12869007..12871275,2	K562	blood:
2	chr18:12869114..12870887-chr18:12882231..12883982,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs2032174	0.86[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap]
rs2292758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.80[ASN][1000 genomes]
rs2847288	0.95[CHD][hapmap];0.89[JPT][hapmap]
rs3826556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs45579734	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs471401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4797707	0.99[ASN][1000 genomes]
rs4797708	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs484020	0.87[MKK][hapmap]
rs502763	0.89[EUR][1000 genomes]
rs507304	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs513185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs578377	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs579052	0.88[AFR][1000 genomes]
rs58200120	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59471125	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs607906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs622717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs637643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6505769	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs669822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs670671	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs683468	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7234029	1.00[ASW][hapmap];0.87[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs7238238	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7241016	1.00[ASW][hapmap];0.83[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap]
rs7241650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73950681	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73950683	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73950684	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73950685	0.82[ASN][1000 genomes]
rs8084365	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8091305	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8098730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9954778	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9959425	0.94[AFR][1000 genomes]
rs9961827	0.85[EUR][1000 genomes]
rs9961931	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9966378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
4	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
5	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12838800-12879000	Weak transcription	Psoas Muscle	Psoas
2	chr18:12844200-12879800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr18:12857400-12872000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr18:12857800-12881600	Weak transcription	Fetal Stomach	stomach
5	chr18:12858000-12872600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr18:12859600-12876800	Weak transcription	Primary T cells from cord blood	blood
7	chr18:12861800-12872600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr18:12862800-12877000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr18:12863000-12872200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr18:12863000-12879000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr18:12863000-12879200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr18:12863200-12879000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr18:12863200-12879800	Weak transcription	Hela-S3	cervix
14	chr18:12863200-12880200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr18:12863400-12872400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr18:12863400-12875400	Weak transcription	HepG2	liver
17	chr18:12863400-12875800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr18:12863400-12879200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr18:12863400-12879800	Weak transcription	NHEK	skin
20	chr18:12863400-12881400	Weak transcription	Right Atrium	heart
21	chr18:12863600-12872000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr18:12863600-12872200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr18:12863600-12875600	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr18:12863600-12876200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr18:12863600-12880000	Weak transcription	Esophagus	oesophagus
26	chr18:12863600-12882000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr18:12863800-12871800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr18:12863800-12872200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr18:12863800-12872200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr18:12863800-12875600	Weak transcription	Primary B cells from peripheral blood	blood
31	chr18:12863800-12878600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr18:12863800-12880000	Weak transcription	Small Intestine	intestine
33	chr18:12863800-12880200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr18:12864400-12876400	Weak transcription	Primary B cells from cord blood	blood
35	chr18:12864400-12876800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr18:12864400-12880000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr18:12864800-12878600	Weak transcription	Lung	lung
38	chr18:12865000-12872400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr18:12865000-12881800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr18:12865200-12879800	Weak transcription	Fetal Lung	lung
41	chr18:12865800-12871800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr18:12865800-12879200	Weak transcription	Pancreas	Pancrea
43	chr18:12865800-12883000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr18:12867600-12870800	Genic enhancers	Fetal Thymus	thymus
45	chr18:12868000-12871200	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr18:12868000-12875800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr18:12868200-12877400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr18:12868400-12877200	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr18:12868600-12872000	Weak transcription	GM12878-XiMat	blood
50	chr18:12868600-12879000	Weak transcription	Rectal Mucosa Donor 31	rectum

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