Variant report

Variant	rs11112993
Chromosome Location	chr12:106831283-106831284
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 149 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs10047654	0.93[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10444532	0.88[EUR][1000 genomes]
rs10507211	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10746060	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778464	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs10778465	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10778466	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778468	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778469	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10778470	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778471	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778473	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778474	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778475	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10778476	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10778478	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10778480	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10778481	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10861577	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs10861578	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs10861579	0.85[EUR][1000 genomes]
rs10861580	0.80[ASN][1000 genomes]
rs10861581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10861582	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10861583	0.82[ASW][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs10861585	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10861586	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10861587	0.82[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs10861588	0.82[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs10861589	0.80[ASN][1000 genomes]
rs10861590	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10861591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10861592	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10861593	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs10861594	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10861595	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10861597	1.00[CHB][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10861598	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10861599	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10861601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10861604	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10861605	0.84[EUR][1000 genomes]
rs10861608	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10861609	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10861613	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11112933	1.00[CHB][hapmap]
rs11112940	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11112943	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11112945	0.85[EUR][1000 genomes]
rs11112948	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11112949	0.87[EUR][1000 genomes]
rs11112951	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11112952	0.82[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs11112953	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs11112957	0.80[ASN][1000 genomes]
rs11112961	0.90[EUR][1000 genomes]
rs11112971	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112979	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112980	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112986	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112990	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11112991	0.82[EUR][1000 genomes]
rs11112992	0.92[EUR][1000 genomes]
rs11112995	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11113004	0.89[EUR][1000 genomes]
rs11113009	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1134577	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11609315	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11611176	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11611252	0.88[ASN][1000 genomes]
rs11611815	0.91[EUR][1000 genomes]
rs11615682	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11835357	0.88[ASN][1000 genomes]
rs12298876	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12305705	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12309708	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12309758	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12312915	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12422988	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12423068	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12424952	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12425459	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17038414	0.90[EUR][1000 genomes]
rs17218490	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17221107	0.84[AFR][1000 genomes]
rs17284674	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17285274	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs1921952	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2141774	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2141775	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2243455	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2288268	0.81[AMR][1000 genomes]
rs2374606	0.81[EUR][1000 genomes]
rs2374610	0.90[EUR][1000 genomes]
rs2888888	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2900499	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2900500	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3851631	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3851632	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3851633	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4509864	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs4625578	0.86[EUR][1000 genomes]
rs55678155	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55689816	0.87[EUR][1000 genomes]
rs60635749	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs61941917	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61941918	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61941920	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61941922	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs61941943	0.81[EUR][1000 genomes]
rs61941944	0.83[EUR][1000 genomes]
rs61943670	0.85[EUR][1000 genomes]
rs61943690	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61943694	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6539268	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6539269	0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6539270	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6539271	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs67911933	0.80[ASN][1000 genomes]
rs67966244	0.92[EUR][1000 genomes]
rs7132744	0.83[EUR][1000 genomes]
rs7132971	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7134615	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7134881	0.82[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap]
rs7135054	0.82[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs7136098	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7137445	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7139139	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7139249	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7297873	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7298062	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7303873	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7306012	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs7306277	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7306326	0.88[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7307711	0.82[AMR][1000 genomes]
rs7308541	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7309020	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7311957	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7313040	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7315549	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7961133	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7963213	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7965520	0.93[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7969743	0.88[ASN][1000 genomes]
rs7971581	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7976305	0.84[AFR][1000 genomes];0.88[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11112993	STAB2	cis	parietal	SCAN
rs11112993	CKAP4	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106774400-106834000	Weak transcription	Small Intestine	intestine
2	chr12:106787600-106856600	Weak transcription	GM12878-XiMat	blood
3	chr12:106787800-106852400	Weak transcription	Gastric	stomach
4	chr12:106787800-106852800	Weak transcription	Pancreas	Pancrea
5	chr12:106802400-106854000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr12:106804800-106832600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:106812000-106855000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:106813000-106839600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:106813000-106864800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:106813200-106852800	Weak transcription	HMEC	breast
11	chr12:106813200-106855800	Weak transcription	NHDF-Ad	bronchial
12	chr12:106813200-106864800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:106813400-106832600	Weak transcription	Osteobl	bone
14	chr12:106814400-106855800	Weak transcription	Stomach Mucosa	stomach
15	chr12:106816200-106833800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:106819400-106839400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:106819400-106839800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:106819400-106855600	Weak transcription	Right Ventricle	heart
19	chr12:106819600-106845000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr12:106819600-106846000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:106821000-106836600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr12:106821200-106833400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:106822000-106832000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:106822000-106852400	Weak transcription	Brain Angular Gyrus	brain
25	chr12:106822000-106853400	Weak transcription	Fetal Brain Female	brain
26	chr12:106822400-106848400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr12:106823000-106831600	Weak transcription	Brain Germinal Matrix	brain
28	chr12:106823000-106832600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:106823000-106838400	Weak transcription	Fetal Brain Male	brain
30	chr12:106823200-106833600	Weak transcription	Colonic Mucosa	Colon
31	chr12:106823200-106839200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:106823200-106858000	Weak transcription	Psoas Muscle	Psoas
33	chr12:106824000-106834800	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:106824200-106835200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:106824800-106866400	Weak transcription	NHLF	lung
36	chr12:106825800-106832000	Strong transcription	Primary T cells from cord blood	blood
37	chr12:106825800-106835400	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr12:106826200-106834800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr12:106826200-106843600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:106826400-106832200	Strong transcription	Primary B cells from cord blood	blood
41	chr12:106826400-106834400	Strong transcription	Placenta	Placenta
42	chr12:106826400-106834600	Strong transcription	Fetal Muscle Trunk	muscle
43	chr12:106826400-106835400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:106826600-106831400	Strong transcription	Ovary	ovary
45	chr12:106826600-106831600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr12:106826600-106834400	Strong transcription	Fetal Muscle Leg	muscle
47	chr12:106826600-106834800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:106826600-106835200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:106826600-106835400	Strong transcription	Duodenum Mucosa	Duodenum
50	chr12:106826800-106835400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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