Variant report

Variant	rs2407438
Chromosome Location	chr4:152089667-152089668
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:152089617-152089890	ProgFib	skin:	n/a	n/a
2	CEBPB	chr4:152089445-152089781	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
SH3D19	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10020317	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10461253	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10461254	0.90[ASN][1000 genomes]
rs10461255	0.91[ASN][1000 genomes]
rs10776522	0.93[ASN][1000 genomes]
rs10857253	0.81[ASN][1000 genomes]
rs11099792	0.81[ASN][1000 genomes]
rs11099793	0.81[ASN][1000 genomes]
rs11733964	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11734577	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11934792	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11938717	0.81[ASN][1000 genomes]
rs11945206	0.83[EUR][1000 genomes]
rs12505974	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12644496	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12647306	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12648512	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13101417	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13111753	0.92[ASN][1000 genomes]
rs13122245	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13122609	0.80[ASN][1000 genomes]
rs13125574	0.93[ASN][1000 genomes]
rs13130167	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13145829	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2280280	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2407222	0.83[EUR][1000 genomes]
rs2407407	0.81[ASN][1000 genomes]
rs2407408	0.81[ASN][1000 genomes]
rs2407409	0.81[ASN][1000 genomes]
rs2407410	0.81[ASN][1000 genomes]
rs2407412	0.81[ASN][1000 genomes]
rs2407417	0.81[ASN][1000 genomes]
rs2407418	0.82[ASN][1000 genomes]
rs2407431	1.00[ASN][1000 genomes]
rs2897655	0.81[ASN][1000 genomes]
rs2897656	0.81[ASN][1000 genomes]
rs2897659	0.81[ASN][1000 genomes]
rs3792611	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4266274	0.94[ASN][1000 genomes]
rs4696234	0.81[ASN][1000 genomes]
rs4696658	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6816613	0.81[ASN][1000 genomes]
rs6816651	0.81[ASN][1000 genomes]
rs6818874	0.81[ASN][1000 genomes]
rs6827056	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6832257	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6844546	0.92[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6846323	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6846981	0.93[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7664483	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7669180	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7691584	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv949002	chr4:151693149-152095109	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv948719	chr4:151693149-152161625	Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv595690	chr4:151788955-152109552	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv1026416	chr4:151847403-152105879	Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv1016220	chr4:151997139-152164126	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv537306	chr4:151997139-152164126	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv964105	chr4:152088312-152090313	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island	1 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	chr4:152027200-152095600	Weak transcription	Pancreas	Pancrea
2	chr4:152043400-152095800	Weak transcription	Placenta	Placenta
3	chr4:152055000-152105800	Weak transcription	Small Intestine	intestine
4	chr4:152062200-152090000	Weak transcription	Brain Anterior Caudate	brain
5	chr4:152065000-152091800	Weak transcription	HMEC	breast
6	chr4:152066000-152095200	Weak transcription	Esophagus	oesophagus
7	chr4:152066200-152092600	Weak transcription	Colonic Mucosa	Colon
8	chr4:152066200-152095800	Weak transcription	Gastric	stomach
9	chr4:152066400-152095800	Weak transcription	Aorta	Aorta
10	chr4:152067000-152090000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:152069200-152090000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr4:152069400-152090000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr4:152070800-152093800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr4:152071000-152090000	Weak transcription	NH-A	brain
15	chr4:152079200-152090000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr4:152079400-152095800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr4:152080400-152090600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr4:152080600-152090800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr4:152082400-152095600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:152083800-152091200	Strong transcription	HepG2	liver
21	chr4:152084000-152093400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr4:152084400-152090400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:152084400-152090600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:152084400-152095600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:152084400-152095800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:152085400-152095400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr4:152085600-152090000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr4:152085600-152090000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:152085600-152090000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr4:152085600-152090800	Weak transcription	NHEK	skin
31	chr4:152085800-152090800	Strong transcription	Fetal Intestine Small	intestine
32	chr4:152085800-152091400	Enhancers	Ovary	ovary
33	chr4:152086600-152092800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:152086800-152092000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:152087000-152090600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:152087200-152090400	Weak transcription	Liver	Liver
37	chr4:152087200-152090400	Weak transcription	Fetal Brain Male	brain
38	chr4:152087400-152090000	Weak transcription	Fetal Kidney	kidney
39	chr4:152087600-152090000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr4:152087600-152090400	Weak transcription	HUVEC	blood vessel
41	chr4:152087600-152095400	Weak transcription	Right Atrium	heart
42	chr4:152088000-152090000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr4:152088000-152096200	Weak transcription	A549	lung
44	chr4:152088000-152101600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr4:152088200-152089800	Weak transcription	NHLF	lung
46	chr4:152088200-152090000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:152088200-152090000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr4:152088200-152090000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:152088200-152090000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr4:152088200-152090000	Weak transcription	Brain Hippocampus Middle	brain

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