Variant report

Variant	rs12644496
Chromosome Location	chr4:152105348-152105349
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10016092	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10020297	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10020317	0.93[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.93[ASN][1000 genomes]
rs10434137	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];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10461254	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10461255	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10520101	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10520102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.81[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];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10857253	0.80[ASW][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs11099781	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs11099792	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11099793	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11099796	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11733964	0.80[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs11734577	0.93[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11934792	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11945206	0.82[ASN][1000 genomes]
rs12505974	0.93[ASW][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[ASN][1000 genomes]
rs12508270	0.85[JPT][hapmap]
rs12647306	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12648512	0.93[ASN][1000 genomes]
rs13101417	0.80[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs13103344	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13111753	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13122245	0.84[ASN][1000 genomes]
rs13122609	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13125574	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13130167	0.85[ASN][1000 genomes]
rs13141515	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs13145829	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs1549512	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs17633530	0.85[JPT][hapmap]
rs17633600	0.85[JPT][hapmap]
rs2280280	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2280283	0.85[JPT][hapmap]
rs2407222	0.82[ASN][1000 genomes]
rs2407223	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2407407	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2407408	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2407409	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2407410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2407412	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]
rs2407413	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[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];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2407418	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2407431	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2407438	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2897655	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2897656	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2897659	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs3736502	0.85[JPT][hapmap]
rs3792611	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4266274	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4312738	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4467540	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4591577	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4696234	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4696239	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4696658	0.93[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs6535764	0.85[JPT][hapmap]
rs6827056	0.84[ASN][1000 genomes]
rs6832257	0.84[ASN][1000 genomes]
rs6846323	0.93[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.87[ASN][1000 genomes]
rs6846981	0.85[ASN][1000 genomes]
rs6847934	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7439970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7656771	0.85[JPT][hapmap]
rs7664483	0.93[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[ASN][1000 genomes]
rs7669180	0.93[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.85[ASN][1000 genomes]
rs7688786	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7691584	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[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	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	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
7	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
8	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
9	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
10	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

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152055000-152105800	Weak transcription	Small Intestine	intestine
2	chr4:152088200-152114600	Weak transcription	Psoas Muscle	Psoas
3	chr4:152090400-152105800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:152091200-152107000	Weak transcription	HSMMtube	muscle
5	chr4:152095800-152105600	Weak transcription	Stomach Mucosa	stomach
6	chr4:152096600-152105600	Weak transcription	Gastric	stomach
7	chr4:152096600-152106200	Weak transcription	Right Ventricle	heart
8	chr4:152096600-152106200	Weak transcription	NHEK	skin
9	chr4:152096600-152118000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:152096800-152106400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:152096800-152106400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:152096800-152120600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:152097200-152106400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:152097200-152123600	Weak transcription	Pancreas	Pancrea
15	chr4:152097200-152136600	Weak transcription	Colonic Mucosa	Colon
16	chr4:152097400-152105800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:152097400-152111600	Weak transcription	Lung	lung
18	chr4:152097400-152123600	Weak transcription	Aorta	Aorta
19	chr4:152097600-152110800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr4:152097600-152111400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:152097600-152111600	Weak transcription	Fetal Stomach	stomach
22	chr4:152097600-152128800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr4:152097800-152105600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr4:152097800-152105800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr4:152097800-152105800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:152097800-152105800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:152097800-152105800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr4:152097800-152106200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:152097800-152110000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:152097800-152111400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:152097800-152117200	Weak transcription	Colon Smooth Muscle	Colon
32	chr4:152097800-152120000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr4:152098000-152105600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr4:152098000-152105800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:152098000-152105800	Weak transcription	HUVEC	blood vessel
36	chr4:152098000-152107400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:152098200-152105600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:152098200-152105600	Weak transcription	Osteobl	bone
39	chr4:152098200-152106000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr4:152098200-152106200	Weak transcription	Left Ventricle	heart
41	chr4:152098200-152106200	Weak transcription	Ovary	ovary
42	chr4:152098200-152106400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr4:152098200-152107000	Weak transcription	Fetal Muscle Trunk	muscle
44	chr4:152098200-152111600	Weak transcription	Fetal Muscle Leg	muscle
45	chr4:152098200-152117000	Weak transcription	Brain Anterior Caudate	brain
46	chr4:152098200-152118400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr4:152098400-152105600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:152098400-152105600	Weak transcription	NHLF	lung
49	chr4:152098400-152105800	Weak transcription	Liver	Liver
50	chr4:152098400-152105800	Weak transcription	NH-A	brain

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