Variant report

Variant	rs12508449
Chromosome Location	chr4:152179738-152179739
allele	C/T
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	RAD21	chr4:152179561-152179913	H1-hESC	embryonic stem cell:	n/a	chr4:152179794-152179813
2	POLR2A	chr4:152179694-152180212	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000249012	TF binding region

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10006091	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10011948	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10012999	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10015834	0.92[EUR][1000 genomes]
rs10016704	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10019075	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10031618	0.93[AMR][1000 genomes]
rs10031902	0.88[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10857257	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11099797	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11099798	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11099799	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11099801	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs11099802	0.94[EUR][1000 genomes]
rs11721421	0.93[EUR][1000 genomes]
rs11726496	0.94[EUR][1000 genomes]
rs11729901	0.88[EUR][1000 genomes]
rs11730707	0.89[EUR][1000 genomes]
rs11733473	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11733501	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11733600	1.00[CEU][hapmap];0.88[YRI][hapmap];0.94[EUR][1000 genomes]
rs11734518	0.94[EUR][1000 genomes]
rs11734727	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735681	0.93[EUR][1000 genomes]
rs12501397	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505382	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13112985	0.83[CEU][hapmap]
rs13117723	0.82[CEU][hapmap]
rs13126069	0.82[CEU][hapmap]
rs1316858	0.82[CEU][hapmap]
rs17590780	0.94[EUR][1000 genomes]
rs2291978	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407166	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28532758	0.82[EUR][1000 genomes]
rs28650996	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28651657	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28767036	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35245353	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3990708	1.00[CEU][hapmap];0.88[YRI][hapmap];0.94[EUR][1000 genomes]
rs4339187	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4385037	0.83[CEU][hapmap]
rs4417949	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4473634	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55812154	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55855806	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55869644	0.94[EUR][1000 genomes]
rs55905531	0.94[EUR][1000 genomes]
rs56220030	0.92[EUR][1000 genomes]
rs62328350	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62328351	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62328353	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6535780	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6535781	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6535782	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6535785	1.00[CEU][hapmap];0.88[YRI][hapmap];0.94[EUR][1000 genomes]
rs6823844	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824159	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824195	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6832149	0.85[CEU][hapmap]
rs6844983	0.87[EUR][1000 genomes]
rs6849871	1.00[CEU][hapmap];0.88[YRI][hapmap];0.94[EUR][1000 genomes]
rs6849875	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6851493	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72725927	0.94[EUR][1000 genomes]
rs7663659	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7665657	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695360	0.88[EUR][1000 genomes]
rs9985620	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9990564	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9994652	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9996742	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9997353	0.86[CEU][hapmap]
rs9997461	0.89[CEU][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
5	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

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152130200-152187800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr4:152149200-152185200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:152149200-152197600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:152156000-152179800	Weak transcription	Fetal Stomach	stomach
5	chr4:152158800-152181800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:152165400-152189000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:152172200-152183400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr4:152172200-152184000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:152172200-152184000	Weak transcription	Lung	lung
10	chr4:152172800-152190600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:152173000-152184000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:152173400-152180600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:152173400-152189400	Weak transcription	Aorta	Aorta
14	chr4:152173800-152198200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:152174000-152187200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:152174000-152192200	Weak transcription	Brain Angular Gyrus	brain
17	chr4:152174200-152183200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr4:152174200-152183400	Weak transcription	Right Atrium	heart
19	chr4:152174200-152183600	Weak transcription	Brain Anterior Caudate	brain
20	chr4:152174400-152183800	Weak transcription	Brain Hippocampus Middle	brain
21	chr4:152174600-152181800	Weak transcription	Left Ventricle	heart
22	chr4:152174600-152182400	Weak transcription	Psoas Muscle	Psoas
23	chr4:152175200-152183600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:152176000-152180000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:152177400-152187600	Weak transcription	Fetal Intestine Large	intestine
26	chr4:152177400-152198200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:152177600-152180600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr4:152177800-152183400	Weak transcription	Colon Smooth Muscle	Colon
29	chr4:152177800-152183600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr4:152177800-152200000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:152178200-152188200	Weak transcription	Liver	Liver
32	chr4:152178600-152180000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:152178800-152180200	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr4:152178800-152180800	Strong transcription	Fetal Intestine Small	intestine
35	chr4:152178800-152181600	Enhancers	Fetal Heart	heart
36	chr4:152179000-152180600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:152179000-152181600	Weak transcription	NHEK	skin
38	chr4:152179200-152180200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr4:152179400-152180200	Genic enhancers	HepG2	liver
40	chr4:152179400-152180800	Enhancers	Right Ventricle	heart
41	chr4:152179400-152183600	Weak transcription	Brain Substantia Nigra	brain
42	chr4:152179600-152180000	Enhancers	Ovary	ovary
43	chr4:152179600-152181000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr4:152179600-152182800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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