Variant report

Variant	rs12623835
Chromosome Location	chr2:99958226-99958227
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr2:99958162-99958401	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
TXNDC9	TF binding region

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10173883	1.00[CEU][hapmap];0.86[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175852	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176205	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179343	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179435	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179697	1.00[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180138	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180688	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182492	0.89[CEU][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs10186223	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10191001	0.88[ASN][1000 genomes]
rs10207435	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210257	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210346	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10469848	0.82[EUR][1000 genomes]
rs10496337	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123776	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11123778	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11123783	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123784	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs12162367	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12617324	0.94[EUR][1000 genomes]
rs12989521	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12991982	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12992356	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13001438	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13017843	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13028722	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13032885	0.84[EUR][1000 genomes]
rs13384665	0.94[ASN][1000 genomes]
rs13394927	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs13401163	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13402784	0.88[CEU][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];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13415713	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13416265	1.00[CEU][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13419448	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13420087	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13420293	0.89[CEU][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs13426758	1.00[CEU][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];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];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429806	1.00[CEU][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13430662	0.81[ASN][1000 genomes]
rs13430962	1.00[CEU][hapmap];0.84[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431410	0.88[CEU][hapmap];0.85[YRI][hapmap]
rs13432046	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565054	0.80[EUR][1000 genomes]
rs17022653	0.89[CEU][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs17022663	0.89[CEU][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs1882598	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1922625	1.00[CEU][hapmap];0.95[YRI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1922626	0.86[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[YRI][hapmap];0.97[AFR][1000 genomes];1.00[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	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382945	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382947	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382955	0.82[EUR][1000 genomes]
rs28745279	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3087399	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792151	0.88[CEU][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs3828162	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4522654	1.00[CEU][hapmap];0.95[YRI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4850902	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851191	0.89[CEU][hapmap]
rs4851197	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4851199	1.00[CEU][hapmap];0.95[YRI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4851201	0.97[AFR][1000 genomes];0.90[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	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6712137	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721031	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726711	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[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];0.95[YRI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72815074	0.82[AFR][1000 genomes];1.00[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[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579143	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[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	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs7581337	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7582085	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582133	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584022	0.88[AFR][1000 genomes];0.90[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	0.80[CEU][hapmap]
rs7599384	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[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];0.95[YRI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7606279	1.00[CEU][hapmap];0.95[YRI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9308819	1.00[CEU][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9308821	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308822	1.00[CEU][hapmap];0.86[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308823	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9973846	0.85[AMR][1000 genomes];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	nsv524466	chr2:99952086-100031551	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12623835	LYG1	cis	Whole Blood	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99954800-99959000	Weak transcription	Lung	lung
2	chr2:99955000-99958400	Enhancers	Liver	Liver
3	chr2:99955000-99959800	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr2:99955000-99964800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:99955000-99965400	Weak transcription	Gastric	stomach
6	chr2:99955000-99977000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:99955000-99979200	Weak transcription	Fetal Stomach	stomach
8	chr2:99955000-99979800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr2:99955200-99961600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:99955200-99974400	Weak transcription	Thymus	Thymus
11	chr2:99955200-99979600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:99955200-99982600	Weak transcription	Fetal Brain Male	brain
13	chr2:99955400-99959000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:99955400-99964400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr2:99955400-99970000	Weak transcription	NHDF-Ad	bronchial
16	chr2:99955400-99976800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:99955400-99979600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr2:99955400-99979600	Weak transcription	NH-A	brain
19	chr2:99955600-99964600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr2:99955600-99978200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:99955800-99961600	Weak transcription	Brain Hippocampus Middle	brain
22	chr2:99955800-99976800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:99956000-99963800	Weak transcription	Primary T cells from cord blood	blood
24	chr2:99956000-99976400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:99956200-99964600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:99956200-99970200	Weak transcription	Osteobl	bone
27	chr2:99956200-99976600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr2:99956200-99977600	Weak transcription	Fetal Thymus	thymus
29	chr2:99956200-100004800	Weak transcription	Fetal Heart	heart
30	chr2:99956400-99962000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:99956400-99962200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr2:99956400-99964400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:99956400-99979600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr2:99956400-99979600	Weak transcription	HUVEC	blood vessel
35	chr2:99956600-99959800	Enhancers	HepG2	liver
36	chr2:99956600-99977200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:99956800-99962400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:99956800-99966800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:99957000-99964000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr2:99957000-99977200	Weak transcription	Dnd41	blood
41	chr2:99957000-99978000	Weak transcription	Small Intestine	intestine
42	chr2:99957400-99978200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:99957600-99958600	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr2:99957600-99960600	Weak transcription	Left Ventricle	heart
45	chr2:99957600-99973000	Weak transcription	Psoas Muscle	Psoas
46	chr2:99957600-99974200	Weak transcription	Pancreas	Pancrea
47	chr2:99957600-99989400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:99957800-99960800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:99957800-99962000	Weak transcription	HMEC	breast
50	chr2:99957800-99978200	Weak transcription	Hela-S3	cervix

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