Variant report

Variant	rs12640376
Chromosome Location	chr4:151648659-151648660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10000193	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10006912	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10013523	0.99[ASN][1000 genomes]
rs10018648	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10027710	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10028965	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10034695	0.98[ASN][1000 genomes]
rs10520078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10857249	0.99[ASN][1000 genomes]
rs10857251	0.97[ASN][1000 genomes]
rs11099775	0.95[ASN][1000 genomes]
rs11726025	0.80[ASN][1000 genomes]
rs11934912	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12505967	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13103081	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13112801	0.88[EUR][1000 genomes]
rs13119454	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13121304	0.99[ASN][1000 genomes]
rs13125957	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13128052	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13130300	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13145181	0.99[ASN][1000 genomes]
rs13145482	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1451633	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1451635	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1470763	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1947315	0.99[ASN][1000 genomes]
rs1993109	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2198190	0.96[ASN][1000 genomes]
rs2407549	0.84[EUR][1000 genomes]
rs4235251	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4318628	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4336207	0.96[ASN][1000 genomes]
rs4455394	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4501201	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696631	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696633	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6822633	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834834	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835970	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6836854	0.84[ASN][1000 genomes]
rs6837840	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6838530	0.97[ASN][1000 genomes]
rs6841524	0.95[ASN][1000 genomes]
rs7665654	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7666190	0.98[ASN][1000 genomes]
rs7672144	0.95[ASN][1000 genomes]
rs7683591	0.94[ASN][1000 genomes]
rs7690485	0.99[ASN][1000 genomes]
rs7690977	0.88[EUR][1000 genomes]
rs7691797	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs896405	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9307879	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9884181	0.99[ASN][1000 genomes]
rs9884963	0.99[ASN][1000 genomes]
rs9996572	0.99[ASN][1000 genomes]
rs9997773	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880256	chr4:151126725-151751369	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv817540	chr4:151228965-151858609	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv869051	chr4:151347901-151737781	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1024820	chr4:151364078-151943561	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1032070	chr4:151514664-151775259	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv830113	chr4:151538184-151691942	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv1029861	chr4:151556384-151720601	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1034948	chr4:151590115-152202687	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv537302	chr4:151590115-152202687	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
10	nsv530159	chr4:151624865-152203910	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151595000-151654800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr4:151639600-151671400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:151640600-151652000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr4:151643600-151654200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr4:151644200-151650600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:151644200-151657400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr4:151644400-151654400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:151644400-151660800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr4:151644400-151660800	Weak transcription	Aorta	Aorta
10	chr4:151644400-151663800	Weak transcription	HMEC	breast
11	chr4:151644600-151664200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr4:151645000-151653600	Weak transcription	HepG2	liver
13	chr4:151645200-151652000	Weak transcription	Lung	lung
14	chr4:151645200-151658200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr4:151645200-151665800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:151645200-151671000	Weak transcription	Left Ventricle	heart
17	chr4:151645400-151650200	Weak transcription	Gastric	stomach
18	chr4:151645400-151651600	Weak transcription	Fetal Stomach	stomach
19	chr4:151645400-151654200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:151645400-151695000	Weak transcription	Esophagus	oesophagus
21	chr4:151645600-151651200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr4:151645600-151651800	Weak transcription	Thymus	Thymus
23	chr4:151645600-151662600	Weak transcription	Pancreas	Pancrea
24	chr4:151645600-151669600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr4:151645600-151690400	Weak transcription	K562	blood
26	chr4:151645600-151749000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr4:151645800-151655800	Weak transcription	Fetal Thymus	thymus
28	chr4:151646000-151652200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr4:151646000-151658400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr4:151646600-151649000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
31	chr4:151646600-151649400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:151646800-151650000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:151647200-151657800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:151647600-151648800	ZNF genes & repeats	Primary T cells from cord blood	blood
35	chr4:151647600-151652000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr4:151647600-151657000	Weak transcription	Brain Hippocampus Middle	brain
37	chr4:151647800-151654400	Weak transcription	Fetal Brain Male	brain
38	chr4:151647800-151677600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr4:151648000-151650400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr4:151648000-151651600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr4:151648000-151651600	Weak transcription	Fetal Lung	lung
42	chr4:151648000-151651600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr4:151648000-151652000	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr4:151648000-151652200	Weak transcription	Liver	Liver
45	chr4:151648000-151652200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr4:151648000-151652400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr4:151648000-151654000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr4:151648000-151655800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr4:151648000-151660800	Weak transcription	GM12878-XiMat	blood
50	chr4:151648000-151664000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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