Variant report

Variant	rs12162367
Chromosome Location	chr2:99935002-99935003
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99929266..99930984-chr2:99932298..99935090,2	K562	blood:

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10173883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175852	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176205	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179343	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179435	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182492	0.90[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs10186223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10191001	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10207435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10469848	0.82[EUR][1000 genomes]
rs10496337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865030	0.80[CEU][hapmap]
rs11123776	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11123778	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11123783	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12617324	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12623835	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989521	0.92[EUR][1000 genomes]
rs12991982	0.86[AFR][1000 genomes]
rs12992356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13001438	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13017843	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13028722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13032885	0.84[EUR][1000 genomes]
rs13384665	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13394927	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs13401163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13402784	0.89[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs13405400	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13415713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13416265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13419448	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13420087	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13420293	0.90[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs13426758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13427424	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13430662	0.81[ASN][1000 genomes]
rs13430962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431410	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap]
rs13432046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565054	0.80[EUR][1000 genomes]
rs17022653	0.90[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs17022663	0.90[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs1882598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1922625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1922626	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs1922627	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1948101	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2309577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309615	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2309616	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28369949	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382945	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382947	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382955	0.82[EUR][1000 genomes]
rs28745279	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3087399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792151	0.89[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs3828162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4522654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4850896	0.82[CEU][hapmap]
rs4850902	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851189	0.80[CEU][hapmap]
rs4851191	0.90[CEU][hapmap]
rs4851197	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4851199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4851201	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851202	0.85[EUR][1000 genomes]
rs62153853	0.86[AFR][1000 genomes]
rs6542877	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6706425	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6712137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721031	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744199	0.87[EUR][1000 genomes]
rs6745645	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749029	1.00[CEU][hapmap];0.92[YRI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72815074	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567230	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7567462	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7569805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579171	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579999	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs7581337	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7582085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584022	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584705	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7585532	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7586635	0.82[CEU][hapmap]
rs7599384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7599843	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7603388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7606279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9308819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9308821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308823	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9973846	0.86[EUR][1000 genomes];0.87[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	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv874699	chr2:99898998-100010044	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv979073	chr2:99927377-99947554	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12162367	LYG1	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99898400-99938600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:99901200-99936600	Weak transcription	Fetal Brain Male	brain
3	chr2:99901600-99941200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:99915000-99942800	Weak transcription	Aorta	Aorta
5	chr2:99917200-99948200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:99919200-99938600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:99921000-99942000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:99921600-99939200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:99922600-99939000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:99928200-99951800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:99931400-99935200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:99932000-99951400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:99933000-99949800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:99933000-99950000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:99933400-99935600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:99933400-99936800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:99933400-99938200	Strong transcription	Primary B cells from cord blood	blood
18	chr2:99933400-99940400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:99933400-99940600	Strong transcription	Left Ventricle	heart
20	chr2:99933400-99945800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr2:99933400-99946800	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr2:99933400-99949000	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr2:99933400-99949600	Strong transcription	Fetal Muscle Leg	muscle
24	chr2:99933400-99949600	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:99933400-99949800	Strong transcription	Duodenum Mucosa	Duodenum
26	chr2:99933400-99950400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:99933400-99950600	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:99933400-99950600	Strong transcription	Fetal Thymus	thymus
29	chr2:99933600-99935400	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:99933600-99935600	Strong transcription	Brain Germinal Matrix	brain
31	chr2:99933600-99935600	Strong transcription	Psoas Muscle	Psoas
32	chr2:99933600-99935800	Strong transcription	Brain Anterior Caudate	brain
33	chr2:99933600-99935800	Strong transcription	HSMMtube	muscle
34	chr2:99933600-99935800	Strong transcription	Osteobl	bone
35	chr2:99933600-99936000	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:99933600-99936400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:99933600-99936800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:99933600-99936800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:99933600-99936800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:99933600-99937000	Strong transcription	Brain Cingulate Gyrus	brain
41	chr2:99933600-99937000	Strong transcription	Ovary	ovary
42	chr2:99933600-99937200	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr2:99933600-99937200	Strong transcription	K562	blood
44	chr2:99933600-99937400	Strong transcription	Fetal Lung	lung
45	chr2:99933600-99938000	Strong transcription	A549	lung
46	chr2:99933600-99939200	Strong transcription	Primary T cells from cord blood	blood
47	chr2:99933600-99939200	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr2:99933600-99949000	Strong transcription	Thymus	Thymus
49	chr2:99933600-99949400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr2:99933600-99949600	Strong transcription	H1 Cell Line	embryonic stem cell

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