Variant report

Variant	rs248257
Chromosome Location	chr5:179408536-179408537
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179403068..179405769-chr5:179408095..179410312,2	K562	blood:

Variant related genes	Relation type
ENSG00000113269	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10036834	0.81[CEU][hapmap]
rs10061480	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes]
rs10068039	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10068529	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10068594	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10078977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10479455	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10479557	0.82[EUR][1000 genomes]
rs10903246	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1102190	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12153541	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs12653944	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs173562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs185076	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs193718	0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs248258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248315	0.87[ASN][1000 genomes]
rs248316	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs248319	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs27013	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[YRI][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs27014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27016	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs27017	0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs27019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2937020	0.88[ASN][1000 genomes]
rs394588	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4130025	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs418384	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4340879	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs4466125	0.80[EUR][1000 genomes]
rs449511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55734821	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62405021	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6871596	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6888883	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7706570	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs857181	0.92[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs857182	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs857183	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs857184	0.86[ASN][1000 genomes]
rs857189	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs864137	0.88[ASN][1000 genomes]
rs864138	0.88[ASN][1000 genomes]
rs9329096	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][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	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179380000-179410800	Weak transcription	Small Intestine	intestine
2	chr5:179381600-179411800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:179383200-179408600	Weak transcription	A549	lung
4	chr5:179389400-179411400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:179392600-179414800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:179396600-179461800	Weak transcription	HSMM	muscle
7	chr5:179400000-179411400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr5:179400400-179412200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr5:179401600-179410400	Strong transcription	Primary hematopoietic stem cells	blood
10	chr5:179402000-179409000	Weak transcription	Fetal Kidney	kidney
11	chr5:179402800-179408600	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr5:179402800-179409000	Weak transcription	Colonic Mucosa	Colon
13	chr5:179404400-179421400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr5:179404600-179410200	Weak transcription	Primary T cells from cord blood	blood
15	chr5:179404600-179439800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:179405200-179409400	Weak transcription	Esophagus	oesophagus
17	chr5:179405200-179410000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr5:179405200-179412200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr5:179405200-179413600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:179405200-179421800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr5:179405200-179428200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:179405200-179429000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:179405200-179453400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr5:179405400-179409200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:179405800-179409200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:179405800-179409200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr5:179405800-179412400	Weak transcription	HSMMtube	muscle
28	chr5:179405800-179414400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr5:179406000-179409200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr5:179406000-179410000	Weak transcription	HepG2	liver
31	chr5:179406000-179412000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr5:179406000-179418400	Weak transcription	Fetal Lung	lung
33	chr5:179406000-179428600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr5:179406200-179409400	Weak transcription	Fetal Intestine Large	intestine
35	chr5:179406200-179411600	Weak transcription	Spleen	Spleen
36	chr5:179406600-179425400	Weak transcription	Colon Smooth Muscle	Colon
37	chr5:179406800-179408600	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr5:179406800-179409200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:179406800-179409400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr5:179406800-179409800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr5:179406800-179410800	Weak transcription	Fetal Muscle Leg	muscle
42	chr5:179406800-179411400	Weak transcription	Fetal Stomach	stomach
43	chr5:179406800-179421600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr5:179407000-179409800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr5:179407000-179428200	Weak transcription	Gastric	stomach
46	chr5:179407200-179409400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr5:179407200-179409400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr5:179407200-179415000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr5:179407400-179411400	Weak transcription	Fetal Muscle Trunk	muscle
50	chr5:179407800-179409400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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