Variant report

Variant	rs10778470
Chromosome Location	chr12:106822654-106822655
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 158 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:156)

rs_ID	r²[population]
rs10047654	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10444532	0.80[EUR][1000 genomes]
rs10507211	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10746059	0.80[ASN][1000 genomes]
rs10746060	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778464	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10778465	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778466	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778468	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778469	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778471	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778473	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778474	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778475	1.00[ASN][1000 genomes]
rs10778476	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778477	0.88[ASN][1000 genomes]
rs10778478	1.00[ASN][1000 genomes]
rs10778480	1.00[ASN][1000 genomes]
rs10778481	1.00[ASN][1000 genomes]
rs10861577	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10861578	0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs10861580	0.92[ASN][1000 genomes]
rs10861581	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10861582	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10861583	0.82[ASW][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10861585	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10861586	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10861587	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10861588	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs10861589	0.92[ASN][1000 genomes]
rs10861590	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10861591	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10861592	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10861593	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10861594	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10861595	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10861597	1.00[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10861598	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10861599	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10861601	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861604	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861605	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10861608	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10861609	1.00[ASN][1000 genomes]
rs10861613	0.96[ASN][1000 genomes]
rs11112933	1.00[CHB][hapmap]
rs11112940	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11112942	0.81[ASN][1000 genomes]
rs11112943	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11112948	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11112949	0.80[ASN][1000 genomes]
rs11112951	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11112952	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11112953	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11112957	0.92[ASN][1000 genomes]
rs11112961	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11112971	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112979	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112980	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112986	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112990	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112991	0.88[ASN][1000 genomes]
rs11112992	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112993	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112995	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11113003	0.88[ASN][1000 genomes]
rs11113004	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11113009	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1134577	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11609315	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11611176	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11611252	1.00[ASN][1000 genomes]
rs11611815	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11615682	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11835357	1.00[ASN][1000 genomes]
rs11835362	0.88[ASN][1000 genomes]
rs12298876	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12305705	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309708	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12309758	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12312915	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12322877	0.89[ASN][1000 genomes]
rs12422988	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12423068	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12424952	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs12425459	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17038414	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17218490	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17284674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17285274	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1921952	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2141774	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2141775	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2243455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2374606	0.88[ASN][1000 genomes]
rs2374610	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28669886	0.81[ASN][1000 genomes]
rs2888888	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs34955444	0.80[ASN][1000 genomes]
rs3851631	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3851632	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851633	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4509864	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs55678155	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55689816	0.80[ASN][1000 genomes]
rs58297001	0.81[ASN][1000 genomes]
rs58767490	0.81[ASN][1000 genomes]
rs60224628	0.81[ASN][1000 genomes]
rs60635749	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61940334	0.81[ASN][1000 genomes]
rs61940335	0.81[ASN][1000 genomes]
rs61940342	0.81[ASN][1000 genomes]
rs61941917	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61941918	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61941920	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61941921	0.88[ASN][1000 genomes]
rs61941922	1.00[ASN][1000 genomes]
rs61941943	0.88[ASN][1000 genomes]
rs61941944	0.88[ASN][1000 genomes]
rs61943672	0.80[ASN][1000 genomes]
rs61943690	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61943693	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61943694	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539268	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539269	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6539270	1.00[ASN][1000 genomes]
rs6539271	1.00[ASN][1000 genomes]
rs67911933	0.92[ASN][1000 genomes]
rs67966244	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7132971	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7134615	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134881	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.84[ASN][1000 genomes]
rs7135054	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7136098	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7137445	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7139139	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139249	1.00[ASN][1000 genomes]
rs7297873	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7298062	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7298462	0.80[ASN][1000 genomes]
rs7303873	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306012	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7306277	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7306326	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7308541	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309020	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310703	0.80[ASN][1000 genomes]
rs7311957	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7313040	0.88[ASN][1000 genomes]
rs7315549	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7961133	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7963213	1.00[ASN][1000 genomes]
rs7965520	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7969743	1.00[ASN][1000 genomes]
rs7971581	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976305	1.00[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	esv3435035	chr12:106765277-107015325	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv832510	chr12:106787730-106951140	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10778470	MAN1A1	trans	parietal	SCAN
rs10778470	STAB2	cis	parietal	SCAN
rs10778470	CKAP4	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106773000-106828000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:106774400-106834000	Weak transcription	Small Intestine	intestine
3	chr12:106787000-106830200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr12:106787600-106856600	Weak transcription	GM12878-XiMat	blood
5	chr12:106787800-106852400	Weak transcription	Gastric	stomach
6	chr12:106787800-106852800	Weak transcription	Pancreas	Pancrea
7	chr12:106788000-106827200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:106789000-106829800	Weak transcription	Brain Hippocampus Middle	brain
9	chr12:106792000-106827800	Weak transcription	Fetal Intestine Large	intestine
10	chr12:106800000-106828200	Weak transcription	K562	blood
11	chr12:106802400-106854000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr12:106803200-106828400	Weak transcription	Fetal Thymus	thymus
13	chr12:106804800-106832600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:106806400-106826800	Weak transcription	Spleen	Spleen
15	chr12:106807200-106828000	Weak transcription	Thymus	Thymus
16	chr12:106808600-106827800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr12:106809200-106830000	Weak transcription	Fetal Kidney	kidney
18	chr12:106809400-106824000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:106810600-106823600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:106810600-106827800	Weak transcription	Fetal Intestine Small	intestine
21	chr12:106811200-106826800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:106811400-106824000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr12:106811400-106824000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr12:106812000-106855000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:106812600-106827000	Weak transcription	A549	lung
26	chr12:106812800-106822800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:106813000-106822800	Weak transcription	Ovary	ovary
28	chr12:106813000-106823400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr12:106813000-106823600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr12:106813000-106823800	Weak transcription	NHLF	lung
31	chr12:106813000-106824000	Weak transcription	NHEK	skin
32	chr12:106813000-106824200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:106813000-106828200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:106813000-106828200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr12:106813000-106828200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr12:106813000-106830000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:106813000-106830000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:106813000-106839600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:106813000-106864800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:106813200-106852800	Weak transcription	HMEC	breast
41	chr12:106813200-106855800	Weak transcription	NHDF-Ad	bronchial
42	chr12:106813200-106864800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr12:106813400-106832600	Weak transcription	Osteobl	bone
44	chr12:106813600-106824200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:106813800-106828000	Weak transcription	NH-A	brain
46	chr12:106813800-106829400	Weak transcription	HUVEC	blood vessel
47	chr12:106814000-106824600	Weak transcription	HSMM	muscle
48	chr12:106814400-106822800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr12:106814400-106855800	Weak transcription	Stomach Mucosa	stomach
50	chr12:106816200-106826400	Weak transcription	Primary hematopoietic stem cells	blood

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