Variant report

Variant	rs2407412
Chromosome Location	chr4:152141399-152141400
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10016092	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10020297	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10020317	0.85[ASW][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[MKK][hapmap];0.80[ASN][1000 genomes]
rs10434137	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10461254	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10461255	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10520101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10520102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10776522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10857253	0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs11099792	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11099793	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11099796	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11733964	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs11734577	0.85[ASW][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.81[ASN][1000 genomes]
rs11934792	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11945206	0.95[ASN][1000 genomes]
rs12505974	0.85[ASW][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs12508270	0.85[JPT][hapmap]
rs12644496	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12647306	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12648512	0.80[ASN][1000 genomes]
rs13101417	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs13103344	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13111753	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13122609	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13125574	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13141515	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs13145829	0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs17633530	0.85[JPT][hapmap]
rs17633600	0.85[JPT][hapmap]
rs2280280	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2280283	0.85[JPT][hapmap]
rs2407222	0.95[ASN][1000 genomes]
rs2407223	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2407407	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407408	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407409	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407413	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2407417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407418	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2407431	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2407438	0.81[ASN][1000 genomes]
rs2897655	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897656	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897659	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs3736502	0.85[JPT][hapmap]
rs3792611	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4266274	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4312738	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4467540	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4591577	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4696234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696239	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4696658	0.85[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs6535764	0.85[JPT][hapmap]
rs6846323	0.85[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap]
rs6847934	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7439970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7656771	0.85[JPT][hapmap]
rs7664483	0.85[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs7669180	0.85[ASW][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap]
rs7688786	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7691584	0.95[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
5	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
6	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
7	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
8	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
9	nsv870229	chr4:152114410-152161072	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152098400-152147200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr4:152117600-152148800	Weak transcription	Esophagus	oesophagus
3	chr4:152118800-152146600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:152120800-152153800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:152124400-152147000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:152124600-152146800	Weak transcription	HSMMtube	muscle
7	chr4:152126400-152147200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr4:152126800-152147000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr4:152128000-152141600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr4:152128400-152146600	Weak transcription	HMEC	breast
11	chr4:152128400-152146800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:152128600-152147200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr4:152129000-152146800	Weak transcription	Brain Angular Gyrus	brain
14	chr4:152129000-152148800	Weak transcription	Fetal Intestine Large	intestine
15	chr4:152129000-152168000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:152129200-152142200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr4:152129200-152148800	Weak transcription	Liver	Liver
18	chr4:152129400-152143800	Weak transcription	Fetal Intestine Small	intestine
19	chr4:152129400-152167800	Weak transcription	Right Ventricle	heart
20	chr4:152129600-152146800	Weak transcription	Fetal Muscle Leg	muscle
21	chr4:152129600-152147200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr4:152130200-152187800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr4:152133600-152147200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr4:152136600-152158000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr4:152137000-152144400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:152137000-152145600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:152137000-152145800	Weak transcription	NH-A	brain
28	chr4:152137000-152146800	Weak transcription	Brain Substantia Nigra	brain
29	chr4:152137000-152147400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr4:152137200-152143800	Weak transcription	Right Atrium	heart
31	chr4:152137400-152146800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr4:152137400-152147200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr4:152137400-152148800	Weak transcription	Left Ventricle	heart
34	chr4:152137600-152146600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:152138800-152142400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr4:152138800-152146800	Weak transcription	Fetal Stomach	stomach
37	chr4:152139000-152142200	Weak transcription	Colon Smooth Muscle	Colon
38	chr4:152139400-152147600	Weak transcription	Fetal Heart	heart
39	chr4:152139800-152143000	Weak transcription	Fetal Lung	lung
40	chr4:152139800-152147200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:152140000-152144200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr4:152140000-152145800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr4:152140000-152146000	Weak transcription	Osteobl	bone
44	chr4:152140200-152145800	Weak transcription	NHLF	lung
45	chr4:152140200-152146800	Weak transcription	NHEK	skin
46	chr4:152140400-152141400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr4:152140400-152142000	Weak transcription	Ovary	ovary
48	chr4:152140400-152144600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr4:152140600-152141400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:152140600-152142000	Weak transcription	Brain Hippocampus Middle	brain

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