Variant report

Variant	rs2412557
Chromosome Location	chr4:55149457-55149458
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10003055	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10004857	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10010509	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10020847	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10021728	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10028020	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10032688	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11133317	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11733839	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11931555	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11935157	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11940889	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13147194	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1547904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1547905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2228230	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276948	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2307050	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2412556	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412558	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28374326	0.87[AMR][1000 genomes]
rs28811736	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3690	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3733540	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4289498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4864872	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864875	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864876	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55732997	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55784333	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60218083	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7677708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9993187	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008793	chr4:55060925-55535807	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking 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	8 gene(s)	inside rSNPs	diseases
2	nsv537098	chr4:55060925-55535807	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1004408	chr4:55124471-55179212	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv537099	chr4:55124471-55179212	Genic enhancers Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv1001094	chr4:55131860-55189739	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv999400	chr4:55143598-55776995	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55121000-55153200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr4:55137400-55161600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:55139000-55153000	Weak transcription	Fetal Kidney	kidney
4	chr4:55143600-55164600	Weak transcription	Colonic Mucosa	Colon
5	chr4:55143800-55150400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:55145000-55150800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
7	chr4:55145600-55163200	Weak transcription	Gastric	stomach
8	chr4:55146600-55149600	Enhancers	Stomach Mucosa	stomach
9	chr4:55147000-55150400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
10	chr4:55147200-55149600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
11	chr4:55147400-55149600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
12	chr4:55147400-55149600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr4:55147600-55149600	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr4:55147600-55150200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:55147600-55156000	Weak transcription	Right Ventricle	heart
16	chr4:55148000-55149600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:55148000-55150000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
18	chr4:55148200-55149800	Enhancers	Pancreas	Pancrea
19	chr4:55148200-55150200	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
20	chr4:55148200-55166000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:55148200-55167200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:55148400-55149600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
23	chr4:55148400-55149800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr4:55148400-55150800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
25	chr4:55148400-55151600	Weak transcription	NH-A	brain
26	chr4:55148400-55152200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr4:55148400-55153200	Weak transcription	Fetal Heart	heart
28	chr4:55148400-55156000	Weak transcription	Adipose Nuclei	Adipose
29	chr4:55148400-55163800	Strong transcription	Ovary	ovary
30	chr4:55148600-55150000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:55148600-55150200	ZNF genes & repeats	Fetal Lung	lung
32	chr4:55148600-55151400	Weak transcription	HUVEC	blood vessel
33	chr4:55148600-55158000	Weak transcription	Colon Smooth Muscle	Colon
34	chr4:55148600-55162600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr4:55148600-55163800	Strong transcription	NHLF	lung
36	chr4:55148600-55166400	Strong transcription	Osteobl	bone
37	chr4:55148800-55149600	Enhancers	HSMMtube	muscle
38	chr4:55148800-55150000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr4:55148800-55161400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:55148800-55162600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:55149000-55149800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr4:55149000-55149800	ZNF genes & repeats	Placenta	Placenta
43	chr4:55149000-55150200	ZNF genes & repeats	Fetal Stomach	stomach
44	chr4:55149000-55150800	ZNF genes & repeats	Fetal Intestine Large	intestine
45	chr4:55149000-55150800	ZNF genes & repeats	Fetal Muscle Leg	muscle
46	chr4:55149200-55149600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
47	chr4:55149200-55149800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr4:55149200-55150400	ZNF genes & repeats	Fetal Intestine Small	intestine
49	chr4:55149400-55150000	Enhancers	Aorta	Aorta
50	chr4:55149400-55162600	Weak transcription	Psoas Muscle	Psoas

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