Variant report

Variant	rs2029162
Chromosome Location	chr3:99984884-99984885
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	chr3:99981876..99985966-chr3:99986124..99992664,8	K562	blood:
2	chr3:99982526..99986006-chr3:99993690..99996529,5	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10936157	0.95[CHB][hapmap]
rs1214371	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1609481	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs2028494	1.00[CHB][hapmap]
rs2316246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs277637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs277656	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs277660	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34547730	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35805111	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35939236	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36013739	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3772698	1.00[CHB][hapmap]
rs384528	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3862050	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4345098	0.88[ASN][1000 genomes]
rs4552390	0.95[CHB][hapmap]
rs4928118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4928119	0.95[CHB][hapmap]
rs4928169	1.00[CHB][hapmap]
rs57048357	1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6804963	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7638503	0.80[ASN][1000 genomes]
rs967608	0.95[CHB][hapmap]
rs9810704	0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9863237	0.86[ASN][1000 genomes]
rs9968163	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv869690	chr3:99984442-100054949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99980600-99988600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:99980600-100037200	Weak transcription	Spleen	Spleen
3	chr3:99980600-100053200	Weak transcription	Gastric	stomach
4	chr3:99980800-99988800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:99981000-99990400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:99981000-99996400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:99981200-99985200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:99981200-99985400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:99981200-99986000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:99981200-99987000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:99981200-99988600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:99981200-99988800	Weak transcription	Fetal Brain Female	brain
13	chr3:99981200-99993200	Weak transcription	Primary B cells from cord blood	blood
14	chr3:99981200-99995400	Weak transcription	Brain Angular Gyrus	brain
15	chr3:99981200-99997800	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr3:99981200-99998400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr3:99981200-99998600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr3:99981200-99998600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:99981200-100004800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:99981200-100030800	Weak transcription	Fetal Heart	heart
21	chr3:99981400-99986800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:99981400-99988600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:99981400-99998400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr3:99981400-100004400	Weak transcription	Lung	lung
25	chr3:99982000-99986800	Weak transcription	Right Atrium	heart
26	chr3:99982200-99990400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:99982400-100005400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:99982600-99998800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr3:99982800-99985000	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr3:99982800-99987200	Weak transcription	Aorta	Aorta
31	chr3:99982800-100001400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:99983000-99985200	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr3:99983000-99986800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:99983000-99987200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:99983000-99987200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:99983000-99988600	Weak transcription	Fetal Muscle Leg	muscle
37	chr3:99983000-99990200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr3:99983000-99995400	Weak transcription	Brain Hippocampus Middle	brain
39	chr3:99983200-99985200	Weak transcription	Psoas Muscle	Psoas
40	chr3:99983200-99985200	Weak transcription	Right Ventricle	heart
41	chr3:99983200-99986800	Weak transcription	Left Ventricle	heart
42	chr3:99983200-99987200	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr3:99983200-99988000	Weak transcription	Ovary	ovary
44	chr3:99983200-99988200	Weak transcription	Fetal Brain Male	brain
45	chr3:99983200-99988600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr3:99983200-99988600	Weak transcription	Small Intestine	intestine
47	chr3:99983200-99999600	Weak transcription	Fetal Intestine Large	intestine
48	chr3:99983200-100010000	Weak transcription	Pancreas	Pancrea
49	chr3:99983400-99986400	Weak transcription	HSMM	muscle
50	chr3:99983400-99987000	Weak transcription	Colon Smooth Muscle	Colon

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