Variant report

Variant	rs10843384
Chromosome Location	chr12:29472409-29472410
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1035604	0.80[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs1052583	0.87[ASW][hapmap];0.84[AFR][1000 genomes]
rs10771508	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10843361	0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap]
rs10843366	0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.86[ASN][1000 genomes]
rs10843367	1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.86[ASN][1000 genomes]
rs10843371	0.89[ASN][1000 genomes]
rs10843377	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10843382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10843403	0.84[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs11050152	0.82[ASN][1000 genomes]
rs11050157	0.84[ASN][1000 genomes]
rs11050161	0.89[ASN][1000 genomes]
rs11050162	0.89[ASN][1000 genomes]
rs11050167	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11050170	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11050173	0.89[ASN][1000 genomes]
rs11050181	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11050187	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050188	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11050189	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11050190	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11050191	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11050192	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11050193	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11050194	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11050200	0.84[AFR][1000 genomes]
rs11050208	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12228468	0.81[CEU][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12231498	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12366505	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12366527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16934135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1989478	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1991114	0.81[ASN][1000 genomes]
rs2042511	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.86[ASN][1000 genomes]
rs2194518	1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.89[ASN][1000 genomes]
rs2194519	0.80[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];0.89[ASN][1000 genomes]
rs2194520	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap]
rs2216853	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2216854	0.95[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap]
rs3764953	0.95[CEU][hapmap];0.83[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3782506	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3782509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3782511	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4331146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57803026	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6487796	0.82[JPT][hapmap];0.89[YRI][hapmap];0.89[ASN][1000 genomes]
rs6487801	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6487804	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6487805	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6487808	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67146951	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67517901	0.89[ASN][1000 genomes]
rs7139273	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs7294598	0.81[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7301188	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7301398	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs7302129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7308125	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[ASN][1000 genomes]
rs7311912	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7312164	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7316004	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs737160	0.94[MEX][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs7954278	1.00[CEU][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7954871	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7957339	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7972032	0.82[ASW][hapmap]
rs7973786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7974221	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7976961	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs918873	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs962866	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs9738721	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10843384	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29426800-29472800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
3	chr12:29452800-29494200	Weak transcription	Lung	lung
4	chr12:29453000-29472800	Weak transcription	Fetal Intestine Large	intestine
5	chr12:29453800-29480000	Weak transcription	Gastric	stomach
6	chr12:29454600-29475800	Weak transcription	Spleen	Spleen
7	chr12:29455200-29489400	Weak transcription	Primary B cells from cord blood	blood
8	chr12:29459400-29493000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr12:29459600-29472800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:29459600-29476000	Weak transcription	Fetal Thymus	thymus
11	chr12:29460200-29476000	Weak transcription	Fetal Stomach	stomach
12	chr12:29461200-29486200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr12:29462600-29533000	Weak transcription	Aorta	Aorta
14	chr12:29463600-29474600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:29463800-29475400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr12:29464000-29476000	Weak transcription	Fetal Kidney	kidney
17	chr12:29464600-29474800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:29465000-29494200	Weak transcription	Colonic Mucosa	Colon
19	chr12:29465800-29472800	Weak transcription	NHDF-Ad	bronchial
20	chr12:29466000-29474400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr12:29466000-29474600	Weak transcription	Placenta	Placenta
22	chr12:29466200-29472600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr12:29466200-29488800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:29467200-29472800	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr12:29467200-29473400	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr12:29467200-29475800	Weak transcription	Pancreas	Pancrea
27	chr12:29467800-29474600	Weak transcription	Adipose Nuclei	Adipose
28	chr12:29468600-29491000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:29469800-29474800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr12:29470000-29475000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:29470000-29475200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:29470000-29475600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:29470000-29475800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:29470000-29486400	Weak transcription	Psoas Muscle	Psoas
35	chr12:29470000-29495600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr12:29470000-29500000	Weak transcription	K562	blood
37	chr12:29470200-29472800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr12:29470200-29472800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr12:29470200-29473000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:29470200-29475000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr12:29470200-29475200	Weak transcription	Primary T cells from cord blood	blood
42	chr12:29470400-29474600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr12:29470400-29474800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr12:29470600-29473000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:29470600-29473000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr12:29470600-29475200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:29470600-29475400	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr12:29470800-29472800	Weak transcription	NH-A	brain
49	chr12:29470800-29473000	Weak transcription	Osteobl	bone
50	chr12:29470800-29474000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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