Variant report

Variant	rs12713270
Chromosome Location	chr2:54832751-54832752
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54798938..54801134-chr2:54831623..54833818,2	K562	blood:
2	chr2:54818759..54820876-chr2:54830874..54833017,2	MCF-7	breast:
3	chr2:54823186..54826195-chr2:54832588..54835705,3	K562	blood:
4	chr2:54829846..54832829-chr2:54836570..54839601,3	MCF-7	breast:

Extended variants
information (count: 113 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10169439	1.00[CEU][hapmap]
rs10170355	1.00[CHB][hapmap]
rs10176359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10176445	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10182836	1.00[CHB][hapmap]
rs10183043	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10183867	1.00[CHB][hapmap]
rs10184128	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs10188185	1.00[CHB][hapmap]
rs10188545	0.81[ASN][1000 genomes]
rs10193692	1.00[CHB][hapmap]
rs10205410	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs10206143	1.00[CHB][hapmap]
rs10210502	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10528	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs1137645	1.00[CHB][hapmap]
rs11555856	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11892236	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11892443	1.00[CHB][hapmap]
rs11896957	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898032	0.82[ASN][1000 genomes]
rs11898033	0.82[ASN][1000 genomes]
rs11902659	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11902987	1.00[CHB][hapmap]
rs11904679	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs12623169	0.85[AFR][1000 genomes]
rs12713262	0.87[EUR][1000 genomes]
rs12713263	0.87[EUR][1000 genomes]
rs12713264	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs12713265	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs12713268	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs12713269	1.00[CHB][hapmap]
rs12713271	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713272	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12713273	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12987967	0.84[EUR][1000 genomes]
rs13004944	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13021606	0.96[EUR][1000 genomes]
rs13021615	0.88[CHB][hapmap]
rs13386146	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs13391522	1.00[CHB][hapmap]
rs13391803	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13399656	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs13403284	1.00[CHB][hapmap]
rs13407214	0.81[ASN][1000 genomes]
rs13408295	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13428703	0.92[CEU][hapmap]
rs17039558	0.84[CEU][hapmap];0.89[CHB][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs17045939	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs17046036	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17046061	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17046067	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17046077	0.85[CHB][hapmap]
rs17046108	0.88[CHB][hapmap]
rs17046257	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs2048370	0.88[CHB][hapmap]
rs2229503	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2271329	0.88[CHB][hapmap]
rs3287	1.00[CHB][hapmap]
rs34077590	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34094680	0.85[EUR][1000 genomes]
rs34308676	0.82[EUR][1000 genomes]
rs34311770	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34978408	0.85[EUR][1000 genomes]
rs354232	0.89[CHB][hapmap]
rs35619551	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3739109	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs3796019	1.00[CHB][hapmap]
rs3796022	0.89[CHB][hapmap];0.82[TSI][hapmap]
rs4261758	0.84[CEU][hapmap];0.89[CHB][hapmap];0.87[TSI][hapmap]
rs4319969	0.89[CHB][hapmap]
rs4346422	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs4347868	0.82[ASN][1000 genomes]
rs4358162	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4374410	0.84[ASN][1000 genomes]
rs4455200	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs4519566	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4577321	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57281248	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58419243	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61126015	0.82[EUR][1000 genomes]
rs6545430	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs6545435	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6545440	0.92[CEU][hapmap]
rs6706263	1.00[CHB][hapmap]
rs67079536	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6708082	0.92[CEU][hapmap]
rs6721612	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724136	0.87[EUR][1000 genomes]
rs67244067	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6730876	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6734445	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6734536	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6739140	0.82[ASN][1000 genomes]
rs6740893	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6741053	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6749802	0.82[ASN][1000 genomes]
rs6752720	0.92[CEU][hapmap]
rs6753004	0.92[CEU][hapmap]
rs7340302	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs7424459	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7556752	1.00[CHB][hapmap]
rs7564719	0.81[ASN][1000 genomes]
rs7569127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7582640	0.92[CEU][hapmap]
rs7584223	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7586066	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7591204	0.81[EUR][1000 genomes]
rs7599241	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7602992	0.86[EUR][1000 genomes]
rs7608414	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[TSI][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12713270	RPL23AP32	cis	cerebellum	SCAN
rs12713270	C2orf63	cis	cerebellum	SCAN
rs12713270	EML6	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54822200-54833800	Genic enhancers	HepG2	liver
2	chr2:54822400-54833600	Enhancers	Psoas Muscle	Psoas
3	chr2:54822400-54833800	Enhancers	Stomach Mucosa	stomach
4	chr2:54822400-54834000	Enhancers	Right Atrium	heart
5	chr2:54824200-54833600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr2:54824600-54834400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:54824800-54834400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:54824800-54839200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:54826800-54834400	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr2:54827200-54833800	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr2:54827200-54834000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:54827200-54839000	Weak transcription	Hela-S3	cervix
13	chr2:54827600-54833000	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr2:54827600-54834000	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr2:54827600-54834000	Enhancers	Right Ventricle	heart
16	chr2:54827600-54834400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:54827600-54834400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr2:54827600-54839200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:54827600-54839200	Weak transcription	Dnd41	blood
20	chr2:54827800-54834000	Enhancers	Brain Anterior Caudate	brain
21	chr2:54827800-54834000	Enhancers	NHDF-Ad	bronchial
22	chr2:54827800-54835600	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr2:54828000-54833000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:54828000-54833000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:54828000-54833200	Enhancers	Small Intestine	intestine
26	chr2:54828000-54833600	Enhancers	Fetal Kidney	kidney
27	chr2:54828000-54834200	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr2:54828200-54833200	Enhancers	Duodenum Mucosa	Duodenum
29	chr2:54828200-54833600	Enhancers	Colon Smooth Muscle	Colon
30	chr2:54828200-54833800	Enhancers	Gastric	stomach
31	chr2:54828200-54833800	Enhancers	Spleen	Spleen
32	chr2:54828200-54834000	Enhancers	Left Ventricle	heart
33	chr2:54828200-54834200	Enhancers	Muscle Satellite Cultured Cells	--
34	chr2:54828200-54834200	Enhancers	Brain Cingulate Gyrus	brain
35	chr2:54828200-54834400	Enhancers	Brain Angular Gyrus	brain
36	chr2:54828400-54833400	Enhancers	Pancreas	Pancrea
37	chr2:54828400-54833800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:54828400-54834000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:54828400-54834200	Enhancers	HUVEC	blood vessel
40	chr2:54828400-54834600	Enhancers	Primary T cells fromperipheralblood	blood
41	chr2:54828800-54832800	Weak transcription	HMEC	breast
42	chr2:54828800-54833000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr2:54828800-54833400	Genic enhancers	Fetal Stomach	stomach
44	chr2:54828800-54833600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:54829000-54833400	Enhancers	NH-A	brain
46	chr2:54829200-54833000	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr2:54829200-54833800	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr2:54829200-54834000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:54829400-54833000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:54829400-54834000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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