Variant report

Variant	rs9857883
Chromosome Location	chr3:157887272-157887273
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:157863466..157866461-chr3:157886047..157887794,2	K562	blood:

Extended variants
information (count: 126 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1095626	0.81[EUR][1000 genomes]
rs1095627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1095628	0.81[EUR][1000 genomes]
rs1095635	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1095637	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1095638	0.80[EUR][1000 genomes]
rs1095639	0.81[EUR][1000 genomes]
rs1095640	0.81[EUR][1000 genomes]
rs1095641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs1095642	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1101158	0.81[EUR][1000 genomes]
rs1104288	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1104289	0.81[EUR][1000 genomes]
rs1193505	0.81[EUR][1000 genomes]
rs1193506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1193507	0.81[EUR][1000 genomes]
rs1193508	0.82[EUR][1000 genomes]
rs1193509	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs1193510	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs1193518	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1193521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1193535	0.80[EUR][1000 genomes]
rs1193537	0.81[EUR][1000 genomes]
rs1204962	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1210359	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs1212739	0.80[EUR][1000 genomes]
rs1213048	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs13060716	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13066362	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs13082553	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13082712	0.86[AMR][1000 genomes]
rs1526191	0.81[EUR][1000 genomes]
rs1526192	0.81[EUR][1000 genomes]
rs1526193	0.81[EUR][1000 genomes]
rs1526194	0.81[EUR][1000 genomes]
rs1618381	0.81[EUR][1000 genomes]
rs1630304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1724652	0.81[EUR][1000 genomes]
rs1724654	0.81[EUR][1000 genomes]
rs1724700	0.81[EUR][1000 genomes]
rs1724704	0.81[EUR][1000 genomes]
rs1730007	1.00[CEU][hapmap];0.94[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs1730020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1730028	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1730040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs1730042	0.81[EUR][1000 genomes]
rs1730045	0.81[EUR][1000 genomes]
rs1730059	0.83[EUR][1000 genomes]
rs1852285	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs1983469	0.82[EUR][1000 genomes]
rs2222326	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2682404	0.81[EUR][1000 genomes]
rs2682405	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs2682406	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2693527	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2693529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2693542	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2698322	0.81[EUR][1000 genomes]
rs2698323	0.81[EUR][1000 genomes]
rs3845981	0.81[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap]
rs4309677	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4679822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441182	0.81[EUR][1000 genomes]
rs6441188	0.85[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs6788703	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs699927	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7610713	0.81[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs7621674	0.81[EUR][1000 genomes]
rs7621971	0.81[EUR][1000 genomes]
rs7626909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637291	0.81[EUR][1000 genomes]
rs7643792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs7651696	1.00[ASN][1000 genomes]
rs7652909	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs827092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs827093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs827094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs827095	0.81[EUR][1000 genomes]
rs827096	0.81[EUR][1000 genomes]
rs827097	0.81[EUR][1000 genomes]
rs827098	0.81[EUR][1000 genomes]
rs827099	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs827101	0.81[EUR][1000 genomes]
rs827106	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs827108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs827109	0.81[EUR][1000 genomes]
rs827110	0.81[EUR][1000 genomes]
rs827111	0.81[EUR][1000 genomes]
rs827113	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs827114	0.81[EUR][1000 genomes]
rs827126	0.81[EUR][1000 genomes]
rs827127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs827128	0.82[EUR][1000 genomes]
rs827129	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs827131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs827132	0.81[EUR][1000 genomes]
rs827134	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs827135	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs827137	0.81[EUR][1000 genomes]
rs827140	0.81[EUR][1000 genomes]
rs827154	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs827163	0.81[EUR][1000 genomes]
rs827164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs827166	0.81[EUR][1000 genomes]
rs827171	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs827176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs827177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs827178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs827179	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs827180	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs827181	0.81[EUR][1000 genomes]
rs844119	0.81[EUR][1000 genomes]
rs864332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs864877	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs865454	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs865455	1.00[CEU][hapmap]
rs9784311	0.82[EUR][1000 genomes]
rs9820370	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9827781	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs9860241	0.95[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9867617	0.84[CHB][hapmap];1.00[JPT][hapmap]

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	nsv1013391	chr3:157505943-158115553	Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv536775	chr3:157505943-158115553	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv829768	chr3:157832878-158012070	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv877689	chr3:157858930-158133307	Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9857883	LXN	cis	parietal	SCAN
rs9857883	LXN	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157846200-157893400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr3:157846200-157893600	Weak transcription	Aorta	Aorta
3	chr3:157846800-157894400	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:157848000-157888200	Weak transcription	Thymus	Thymus
5	chr3:157849400-157894400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:157854600-157911800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:157856200-157894400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr3:157856400-157892400	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:157868200-157916200	Weak transcription	Primary B cells from cord blood	blood
10	chr3:157869400-157887600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:157873200-157902000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:157874000-157889600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:157879200-157896000	Weak transcription	Pancreas	Pancrea
14	chr3:157883200-157887800	Enhancers	Hela-S3	cervix
15	chr3:157883200-157887800	Enhancers	Osteobl	bone
16	chr3:157883400-157887800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:157884400-157894800	Weak transcription	Fetal Thymus	thymus
18	chr3:157885000-157889000	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:157885200-157887400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:157885200-157887400	Enhancers	HSMM	muscle
21	chr3:157885200-157887600	Enhancers	HSMMtube	muscle
22	chr3:157885200-157887600	Enhancers	NH-A	brain
23	chr3:157885200-157889600	Weak transcription	Psoas Muscle	Psoas
24	chr3:157885400-157887600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:157885400-157887600	Enhancers	HMEC	breast
26	chr3:157885400-157887800	Enhancers	Muscle Satellite Cultured Cells	--
27	chr3:157885400-157889000	Enhancers	Stomach Mucosa	stomach
28	chr3:157885600-157887400	Strong transcription	Primary T cells from cord blood	blood
29	chr3:157885600-157887400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:157886000-157887600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:157886000-157887600	Enhancers	K562	blood
32	chr3:157886000-157887800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:157886000-157888000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr3:157886000-157888600	Weak transcription	GM12878-XiMat	blood
35	chr3:157886000-157899200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:157886200-157890200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:157886800-157887600	Enhancers	Ovary	ovary
38	chr3:157886800-157887800	Enhancers	Fetal Heart	heart
39	chr3:157887000-157887400	Flanking Active TSS	A549	lung
40	chr3:157887000-157888200	Weak transcription	Dnd41	blood
41	chr3:157887000-157889000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:157887000-157890800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:157887000-157892400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:157887000-157893600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:157887000-157894200	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr3:157887000-157894800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr3:157887000-157916400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr3:157887200-157888400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:157887200-157889800	Weak transcription	NHEK	skin
50	chr3:157887200-157891800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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