Variant report

Variant	rs2583401
Chromosome Location	chr4:102204529-102204530
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1031033	0.86[JPT][hapmap]
rs1031034	0.86[JPT][hapmap]
rs1348161	0.86[JPT][hapmap]
rs1441433	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1530259	0.86[JPT][hapmap]
rs1561719	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2028475	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2099813	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2583389	0.86[JPT][hapmap]
rs2583392	0.86[JPT][hapmap]
rs2583394	0.86[JPT][hapmap]
rs2583395	0.86[JPT][hapmap]
rs2583398	0.86[JPT][hapmap]
rs2583399	0.86[JPT][hapmap]
rs2583400	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2583402	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2583406	0.87[CEU][hapmap];0.91[JPT][hapmap];0.97[EUR][1000 genomes]
rs2583410	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2659501	0.82[MEX][hapmap]
rs2850326	0.86[JPT][hapmap]
rs2850332	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2850339	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2850344	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850348	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850349	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850350	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850351	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850352	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850354	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2850355	0.93[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850356	0.93[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850357	0.97[EUR][1000 genomes]
rs2850358	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850360	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850367	0.86[JPT][hapmap]
rs2850370	0.86[JPT][hapmap]
rs2850371	0.86[JPT][hapmap]
rs2850954	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2850963	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2850967	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2850969	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2850974	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2850975	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2850976	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3804420	0.82[JPT][hapmap]
rs755961	0.94[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs920559	0.93[CEU][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes]
rs920560	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs962384	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv879676	chr4:102202285-102340930	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102192800-102208600	Weak transcription	Fetal Kidney	kidney
2	chr4:102194000-102205200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:102198400-102206800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:102198800-102207800	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr4:102199600-102205200	Enhancers	Primary B cells from peripheral blood	blood
6	chr4:102199600-102210400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr4:102199800-102206800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:102200000-102211800	Weak transcription	HMEC	breast
9	chr4:102200200-102206200	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr4:102200600-102211800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:102200800-102206200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:102200800-102206200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:102200800-102209000	Weak transcription	Aorta	Aorta
14	chr4:102201000-102206200	Weak transcription	Ovary	ovary
15	chr4:102201000-102206800	Weak transcription	Gastric	stomach
16	chr4:102201000-102207000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr4:102201000-102213000	Weak transcription	Fetal Heart	heart
18	chr4:102201200-102205200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:102201200-102205200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:102201200-102205600	Weak transcription	HUVEC	blood vessel
21	chr4:102201200-102207800	Weak transcription	Adipose Nuclei	Adipose
22	chr4:102201200-102218200	Weak transcription	NHEK	skin
23	chr4:102201400-102204800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:102201400-102205000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:102201400-102205200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:102201400-102205400	Weak transcription	A549	lung
27	chr4:102201400-102206000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr4:102201400-102206200	Weak transcription	NH-A	brain
29	chr4:102201400-102206800	Weak transcription	Osteobl	bone
30	chr4:102201400-102214200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr4:102201600-102206000	Weak transcription	NHDF-Ad	bronchial
32	chr4:102201600-102206000	Weak transcription	NHLF	lung
33	chr4:102201600-102206200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr4:102201600-102206800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:102202000-102205000	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr4:102202200-102210600	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr4:102202400-102205200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:102202400-102205600	Enhancers	Primary T cells from cord blood	blood
39	chr4:102202400-102205600	Weak transcription	Colon Smooth Muscle	Colon
40	chr4:102202400-102205800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:102202400-102209200	Weak transcription	Brain Substantia Nigra	brain
42	chr4:102202600-102205000	Weak transcription	Brain Anterior Caudate	brain
43	chr4:102202600-102208600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr4:102202800-102206000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr4:102203000-102204600	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr4:102203000-102205200	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr4:102203000-102206000	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr4:102203000-102206200	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr4:102203000-102207800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr4:102203200-102204800	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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