Variant report

Variant	rs12126607
Chromosome Location	chr1:76217097-76217098
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:76189684..76191516-chr1:76216756..76219310,2	K562	blood:
2	chr1:76197492..76199222-chr1:76216070..76218442,2	K562	blood:
3	chr1:76205678..76212783-chr1:76212896..76217702,9	K562	blood:
4	chr1:76216562..76219255-chr1:76235194..76236750,2	K562	blood:
5	chr1:76213109..76217378-chr1:76260068..76263795,4	K562	blood:

Variant related genes	Relation type
ENSG00000117054	Chromatin interaction
ENSG00000057468	Chromatin interaction
ENSG00000181227	Chromatin interaction
ENSG00000178193	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1061337	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873685	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161437	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11161468	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161493	1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161510	1.00[CHB][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161511	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161515	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161521	1.00[CHB][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163924	0.86[EUR][1000 genomes]
rs1146574	1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146579	1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146580	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146581	1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146588	1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091720	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12094842	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12123977	1.00[CHB][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126481	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127402	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134854	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12136754	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1250874	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251075	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1303169	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1313071	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498312	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1498315	1.00[CHB][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1498316	0.89[EUR][1000 genomes]
rs1498317	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1611823	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1612097	1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1613437	0.80[EUR][1000 genomes]
rs1694419	1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1694424	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17587071	1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1767455	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1767456	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1767458	1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770511	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1855136	0.90[EUR][1000 genomes]
rs1858536	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1890451	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890452	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066183	1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs211717	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs211718	0.82[EUR][1000 genomes]
rs2153126	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173378	1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185152	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2185435	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185436	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211080	1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs2275378	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2788654	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28602663	0.93[EUR][1000 genomes]
rs3818855	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4559448	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949872	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4949874	1.00[CHB][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4949875	1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs4949876	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4949877	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949879	0.92[EUR][1000 genomes]
rs56267813	0.84[EUR][1000 genomes]
rs56352044	0.84[EUR][1000 genomes]
rs57186386	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745328	1.00[JPT][hapmap]
rs60378926	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs61289992	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61622554	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61797339	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61797340	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61799967	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61799988	0.88[EUR][1000 genomes]
rs61799990	0.89[EUR][1000 genomes]
rs6593514	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593515	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593585	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6688749	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72686191	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7513363	0.84[EUR][1000 genomes]
rs7513559	1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs7516122	0.87[EUR][1000 genomes]
rs7516226	0.93[EUR][1000 genomes]
rs7518038	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7524467	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533888	1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7534754	1.00[CHB][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7535991	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7539246	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541058	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544117	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7546641	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7548962	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7549167	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7550974	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552404	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7554984	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8763	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs942270	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9662166	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830281	chr1:76095292-76251053	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12126607	MSH4	cis	Artery Tibial	GTEx
rs12126607	ACADM	cis	Muscle Skeletal	GTEx
rs12126607	ACADM	cis	Whole Blood	GTEx
rs12126607	ACADM	cis	Esophagus Muscularis	GTEx
rs12126607	MSH4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76191200-76219600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:76192000-76220400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:76192000-76220600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:76192000-76227800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:76192200-76217800	Weak transcription	Fetal Brain Male	brain
6	chr1:76192200-76222000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:76193600-76220200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:76193800-76220200	Weak transcription	Fetal Heart	heart
9	chr1:76195600-76219600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:76196000-76222000	Strong transcription	Liver	Liver
11	chr1:76197600-76219400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:76199600-76218600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:76199600-76220400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:76201600-76217800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:76202000-76225000	Weak transcription	Stomach Mucosa	stomach
16	chr1:76203400-76230800	Weak transcription	NHDF-Ad	bronchial
17	chr1:76204800-76229000	Weak transcription	Psoas Muscle	Psoas
18	chr1:76208600-76223800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:76208800-76220400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:76208800-76231400	Weak transcription	A549	lung
21	chr1:76208800-76231400	Weak transcription	NHEK	skin
22	chr1:76208800-76231600	Weak transcription	Hela-S3	cervix
23	chr1:76209000-76220200	Weak transcription	Fetal Kidney	kidney
24	chr1:76209000-76230800	Weak transcription	HUVEC	blood vessel
25	chr1:76209000-76230800	Weak transcription	NHLF	lung
26	chr1:76209400-76217600	Weak transcription	HepG2	liver
27	chr1:76209400-76220400	Weak transcription	Colonic Mucosa	Colon
28	chr1:76210000-76218600	Weak transcription	Small Intestine	intestine
29	chr1:76210200-76217200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:76210200-76217600	Weak transcription	Primary B cells from cord blood	blood
31	chr1:76210200-76217600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr1:76210200-76220200	Weak transcription	Right Ventricle	heart
33	chr1:76210200-76220400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr1:76210200-76223000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr1:76210200-76231800	Weak transcription	HSMMtube	muscle
36	chr1:76210400-76217200	Weak transcription	Gastric	stomach
37	chr1:76210400-76217200	Weak transcription	Thymus	Thymus
38	chr1:76210400-76219600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr1:76210400-76219600	Weak transcription	Aorta	Aorta
40	chr1:76210400-76220200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr1:76210400-76220200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:76210600-76217200	Weak transcription	Brain Germinal Matrix	brain
43	chr1:76210600-76220000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:76210600-76220200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr1:76210600-76220400	Weak transcription	Brain Angular Gyrus	brain
46	chr1:76210600-76220400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr1:76210600-76220400	Weak transcription	Esophagus	oesophagus
48	chr1:76211200-76217200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:76211200-76220200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:76211400-76217400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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