Variant report

Variant	rs4760740
Chromosome Location	chr12:49081525-49081526
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49079263..49083026-chr12:49101907..49104961,3	K562	blood:
2	chr12:49079132..49081728-chr12:49082778..49085110,2	K562	blood:
3	chr12:49072887..49077758-chr12:49080125..49086735,20	MCF-7	breast:
4	chr12:49080142..49082217-chr12:49109244..49111484,3	K562	blood:
5	chr12:49080816..49082790-chr12:49089685..49091197,2	K562	blood:
6	chr12:49080316..49082217-chr12:49109829..49111484,2	K562	blood:
7	chr12:49081356..49082903-chr12:49083165..49085083,2	MCF-7	breast:
8	chr12:49081164..49084548-chr12:49085177..49089897,6	K562	blood:
9	chr12:49079263..49083026-chr12:49101684..49104961,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000129315	Chromatin interaction
ENSG00000139620	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10747554	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10783273	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10783274	0.87[ASN][1000 genomes]
rs10783275	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10783277	0.88[CEU][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs10783278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783281	0.86[EUR][1000 genomes]
rs10875849	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs10875850	0.92[ASN][1000 genomes]
rs10875852	0.97[ASN][1000 genomes]
rs10875853	0.97[ASN][1000 genomes]
rs10875861	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875862	0.93[ASN][1000 genomes]
rs1110432	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168657	0.90[ASN][1000 genomes]
rs11168665	0.97[ASN][1000 genomes]
rs11168674	0.95[ASN][1000 genomes]
rs11168697	0.85[ASN][1000 genomes]
rs11168698	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11168702	0.81[JPT][hapmap]
rs12299955	0.89[ASN][1000 genomes]
rs12426435	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1316514	0.91[ASN][1000 genomes]
rs1863541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1895995	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2114320	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2162317	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2277365	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2277366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291728	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2409085	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2898087	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3209584	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35717253	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3741628	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3741629	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3741630	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741632	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3803025	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3943899	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4113946	0.92[ASN][1000 genomes]
rs4500528	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4760735	0.92[ASN][1000 genomes]
rs4760737	0.93[ASN][1000 genomes]
rs4760739	0.91[ASN][1000 genomes]
rs6580689	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6580690	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6580692	0.82[EUR][1000 genomes]
rs6580693	0.90[EUR][1000 genomes]
rs7133756	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap]
rs7136021	0.81[ASN][1000 genomes]
rs7138190	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7138930	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs7139236	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299276	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304711	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7305907	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7306604	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7308699	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7314665	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7954446	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7954548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]
rs7964546	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7966065	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7973824	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7974151	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7974625	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7975030	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7975821	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9332441	0.96[ASN][1000 genomes]
rs9634241	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9634242	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9634262	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332169	chr12:49005807-49150691	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4760740	SNORA2B	cis	cerebellum	SCAN
rs4760740	ADCY6	cis	parietal	SCAN
rs4760740	ZNF641	cis	cerebellum	SCAN
rs4760740	WNT10B	cis	Muscle Skeletal	GTEx
rs4760740	FAM186B	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49076000-49087000	Weak transcription	Stomach Mucosa	stomach
2	chr12:49076400-49083200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:49076600-49081600	Weak transcription	Osteobl	bone
4	chr12:49076600-49081800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:49076600-49081800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr12:49076600-49082200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:49076600-49082200	Weak transcription	Fetal Brain Male	brain
8	chr12:49076600-49082200	Weak transcription	Left Ventricle	heart
9	chr12:49076600-49082200	Weak transcription	NHDF-Ad	bronchial
10	chr12:49076600-49082400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:49076600-49082400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:49076600-49082400	Weak transcription	Fetal Lung	lung
13	chr12:49076600-49082600	Weak transcription	Brain Angular Gyrus	brain
14	chr12:49076600-49082600	Weak transcription	Brain Substantia Nigra	brain
15	chr12:49076600-49082800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:49076600-49083600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr12:49076600-49083800	Weak transcription	Lung	lung
18	chr12:49076600-49084200	Weak transcription	Fetal Muscle Leg	muscle
19	chr12:49076600-49084200	Weak transcription	Psoas Muscle	Psoas
20	chr12:49076600-49084200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:49076600-49084200	Weak transcription	Small Intestine	intestine
22	chr12:49076600-49084200	Weak transcription	NHLF	lung
23	chr12:49076600-49084800	Weak transcription	Colonic Mucosa	Colon
24	chr12:49076600-49085600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:49076600-49086400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:49076600-49086400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr12:49076600-49086400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr12:49076600-49086400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:49076600-49086600	Weak transcription	Fetal Kidney	kidney
30	chr12:49076600-49086800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:49076600-49086800	Weak transcription	Aorta	Aorta
32	chr12:49076600-49086800	Weak transcription	Esophagus	oesophagus
33	chr12:49076600-49086800	Weak transcription	Gastric	stomach
34	chr12:49076600-49086800	Weak transcription	Ovary	ovary
35	chr12:49076600-49086800	Weak transcription	Pancreas	Pancrea
36	chr12:49076600-49086800	Weak transcription	Spleen	Spleen
37	chr12:49076600-49096400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:49076600-49109000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:49076800-49081600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:49076800-49081600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:49076800-49081600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:49076800-49081800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr12:49076800-49081800	Weak transcription	Fetal Stomach	stomach
44	chr12:49076800-49082000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr12:49076800-49082200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:49076800-49082200	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr12:49076800-49082200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr12:49076800-49082200	Weak transcription	Brain Germinal Matrix	brain
49	chr12:49076800-49082400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:49076800-49082400	Weak transcription	Primary T cells fromperipheralblood	blood

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