Variant report

Variant	rs2153126
Chromosome Location	chr1:76199345-76199346
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:76199337-76199432	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:76195849..76201919-chr1:76251987..76255873,8	K562	blood:
2	chr1:76198750..76201093-chr1:76210401..76212796,3	K562	blood:
3	chr1:76197028..76199654-chr1:76253368..76256114,2	K562	blood:
4	chr1:76188769..76191418-chr1:76197121..76200007,3	MCF-7	breast:
5	chr1:76196771..76202637-chr1:76258126..76262356,7	K562	blood:
6	chr1:76197560..76200556-chr1:76208948..76211290,2	K562	blood:

No data

Variant related genes	Relation type
ACADM	TF binding region
ENSG00000207241	Chromatin interaction
ENSG00000206620	Chromatin interaction
ENSG00000137955	Chromatin interaction
ENSG00000181227	Chromatin interaction
ENSG00000201487	Chromatin interaction
ENSG00000178193	Chromatin interaction
ENSG00000117054	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1061337	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873685	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161437	0.91[EUR][1000 genomes]
rs11161468	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161493	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161510	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161511	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161515	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161521	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163924	0.81[EUR][1000 genomes]
rs1146574	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146579	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146580	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146581	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146588	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091720	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12094842	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12123977	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126481	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126607	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127402	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134854	0.82[EUR][1000 genomes]
rs12136754	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1250874	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251075	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251077	0.87[AFR][1000 genomes]
rs1251078	0.90[AFR][1000 genomes]
rs1251079	0.90[AFR][1000 genomes]
rs1303169	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1313071	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498312	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1498315	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1498316	0.84[EUR][1000 genomes]
rs1498317	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1611823	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1612097	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1613437	0.87[EUR][1000 genomes]
rs1694419	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1694424	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17587071	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1767455	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1767456	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1767458	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770511	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1855136	0.85[EUR][1000 genomes]
rs1858536	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1890451	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890452	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066183	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2173378	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185152	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2185435	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185436	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211080	0.82[EUR][1000 genomes]
rs2275378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2788654	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28602663	0.87[EUR][1000 genomes]
rs3818855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4559448	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646961	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949674	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949874	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4949875	0.87[EUR][1000 genomes]
rs4949876	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4949877	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949879	0.86[EUR][1000 genomes]
rs57186386	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60378926	0.81[EUR][1000 genomes]
rs61289992	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61622554	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61797339	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61797340	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61799967	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61799969	0.86[EUR][1000 genomes]
rs61799988	0.81[EUR][1000 genomes]
rs61799990	0.82[EUR][1000 genomes]
rs6593514	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593515	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593585	0.83[EUR][1000 genomes]
rs6688749	0.86[EUR][1000 genomes]
rs72686191	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7513363	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7513559	0.88[EUR][1000 genomes]
rs7515955	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7516122	0.82[EUR][1000 genomes]
rs7516226	0.87[EUR][1000 genomes]
rs7518038	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7524467	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533888	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7534754	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7535991	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7539246	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541058	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544117	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7546641	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7548962	0.83[EUR][1000 genomes]
rs7549167	0.83[EUR][1000 genomes]
rs7550974	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552404	0.83[EUR][1000 genomes]
rs7554984	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8763	0.93[ASN][1000 genomes]
rs942270	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9662166	0.86[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	nsv870520	chr1:76088392-76206490	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	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
4	nsv871572	chr1:76161889-76208488	Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2153126	MSH4	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76190800-76199400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:76190800-76207200	Weak transcription	Spleen	Spleen
3	chr1:76190800-76208000	Weak transcription	Gastric	stomach
4	chr1:76191200-76219600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:76191400-76199400	Weak transcription	Aorta	Aorta
6	chr1:76191800-76208000	Weak transcription	A549	lung
7	chr1:76191800-76208200	Weak transcription	Brain Substantia Nigra	brain
8	chr1:76191800-76209400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr1:76192000-76199400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:76192000-76199400	Weak transcription	Lung	lung
11	chr1:76192000-76208000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:76192000-76210200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:76192000-76220400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:76192000-76220600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr1:76192000-76227800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:76192200-76200000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:76192200-76200200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:76192200-76200400	Weak transcription	Placenta	Placenta
19	chr1:76192200-76204600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:76192200-76217800	Weak transcription	Fetal Brain Male	brain
21	chr1:76192200-76222000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr1:76192400-76199400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:76192400-76199400	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:76192400-76199400	Weak transcription	Thymus	Thymus
25	chr1:76192400-76199600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:76192400-76200200	Weak transcription	HMEC	breast
27	chr1:76192400-76200200	Weak transcription	HUVEC	blood vessel
28	chr1:76192400-76200600	Weak transcription	Brain Angular Gyrus	brain
29	chr1:76192400-76200600	Weak transcription	Fetal Kidney	kidney
30	chr1:76192400-76200600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:76192400-76201200	Weak transcription	Stomach Mucosa	stomach
32	chr1:76192400-76207600	Weak transcription	Colonic Mucosa	Colon
33	chr1:76192600-76199400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr1:76193000-76199600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr1:76193600-76220200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:76193800-76199400	Weak transcription	Fetal Brain Female	brain
37	chr1:76193800-76200400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr1:76193800-76200600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:76193800-76200600	Weak transcription	Esophagus	oesophagus
40	chr1:76193800-76200600	Weak transcription	Pancreas	Pancrea
41	chr1:76193800-76207800	Weak transcription	Right Ventricle	heart
42	chr1:76193800-76208000	Weak transcription	Hela-S3	cervix
43	chr1:76193800-76208600	Weak transcription	Small Intestine	intestine
44	chr1:76193800-76220200	Weak transcription	Fetal Heart	heart
45	chr1:76194000-76200400	Weak transcription	Brain Germinal Matrix	brain
46	chr1:76194000-76208000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr1:76195600-76219600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:76195800-76201200	Strong transcription	Primary B cells from cord blood	blood
49	chr1:76195800-76213800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:76196000-76210800	Strong transcription	Primary B cells from peripheral blood	blood

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