Variant report

Variant	rs2185435
Chromosome Location	chr1:76203764-76203765
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:76189536..76192375-chr1:76202654..76205815,3	K562	blood:
2	chr1:76203557..76205358-chr1:76211524..76214025,2	K562	blood:
3	chr1:76195178..76198710-chr1:76202418..76206872,5	K562	blood:
4	chr1:76197210..76199474-chr1:76201595..76205002,3	K562	blood:

Variant related genes	Relation type
ENSG00000178193	Chromatin interaction
ENSG00000117054	Chromatin interaction

Extended variants
information (count: 109 )
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	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161437	0.91[EUR][1000 genomes]
rs11161468	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161493	0.95[AFR][1000 genomes];0.95[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	0.86[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	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146579	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146580	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146581	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146588	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091720	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12094842	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12123977	0.86[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	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127402	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134854	0.82[EUR][1000 genomes]
rs12136754	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1250874	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251075	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251077	0.90[AFR][1000 genomes]
rs1251078	0.87[AFR][1000 genomes]
rs1251079	0.87[AFR][1000 genomes]
rs1303169	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1313071	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498312	0.91[EUR][1000 genomes]
rs1498315	0.89[EUR][1000 genomes]
rs1498316	0.84[EUR][1000 genomes]
rs1498317	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1611823	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1612097	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1613437	0.87[EUR][1000 genomes]
rs1694419	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1694424	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17587071	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1767455	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1767456	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1767458	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770511	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1855136	0.85[EUR][1000 genomes]
rs1858536	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1890451	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890452	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066183	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2153126	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173378	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185152	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2185436	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211080	0.82[EUR][1000 genomes]
rs2275378	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2788654	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28602663	0.87[EUR][1000 genomes]
rs3818855	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4559448	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646961	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949674	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949874	0.89[EUR][1000 genomes]
rs4949875	0.87[EUR][1000 genomes]
rs4949876	0.90[EUR][1000 genomes]
rs4949877	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949879	0.86[EUR][1000 genomes]
rs57186386	0.96[AFR][1000 genomes];0.96[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	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61797339	0.80[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	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593515	0.96[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	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7513559	0.88[EUR][1000 genomes]
rs7515955	0.83[EUR][1000 genomes]
rs7516122	0.82[EUR][1000 genomes]
rs7516226	0.87[EUR][1000 genomes]
rs7518038	0.88[EUR][1000 genomes]
rs7524467	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533888	0.88[EUR][1000 genomes]
rs7534754	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7535991	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7539246	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541058	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544117	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7546641	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7548962	0.83[EUR][1000 genomes]
rs7549167	0.83[EUR][1000 genomes]
rs7550974	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552404	0.83[EUR][1000 genomes]
rs7554984	0.96[AFR][1000 genomes];0.94[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:6 , 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
5	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
6	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2185435	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	chr1:76190800-76207200	Weak transcription	Spleen	Spleen
2	chr1:76190800-76208000	Weak transcription	Gastric	stomach
3	chr1:76191200-76219600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:76191800-76208000	Weak transcription	A549	lung
5	chr1:76191800-76208200	Weak transcription	Brain Substantia Nigra	brain
6	chr1:76191800-76209400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:76192000-76208000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:76192000-76210200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:76192000-76220400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:76192000-76220600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:76192000-76227800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:76192200-76204600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:76192200-76217800	Weak transcription	Fetal Brain Male	brain
14	chr1:76192200-76222000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:76192400-76207600	Weak transcription	Colonic Mucosa	Colon
16	chr1:76193600-76220200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:76193800-76207800	Weak transcription	Right Ventricle	heart
18	chr1:76193800-76208000	Weak transcription	Hela-S3	cervix
19	chr1:76193800-76208600	Weak transcription	Small Intestine	intestine
20	chr1:76193800-76220200	Weak transcription	Fetal Heart	heart
21	chr1:76194000-76208000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:76195600-76219600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:76195800-76213800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:76196000-76210800	Strong transcription	Primary B cells from peripheral blood	blood
25	chr1:76196000-76222000	Strong transcription	Liver	Liver
26	chr1:76196200-76212600	Strong transcription	Fetal Thymus	thymus
27	chr1:76196400-76210800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:76196400-76213000	Strong transcription	Dnd41	blood
29	chr1:76197600-76209600	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr1:76197600-76211400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:76197600-76212000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:76197600-76219400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:76197800-76204200	Weak transcription	Psoas Muscle	Psoas
34	chr1:76197800-76207400	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:76197800-76210600	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:76198000-76210400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr1:76198200-76209800	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr1:76198200-76210400	Strong transcription	Adipose Nuclei	Adipose
39	chr1:76198200-76210600	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr1:76198400-76210400	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:76198600-76205400	Strong transcription	Fetal Muscle Leg	muscle
42	chr1:76198600-76208000	Weak transcription	NHLF	lung
43	chr1:76198600-76210200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr1:76198600-76210400	Strong transcription	Duodenum Mucosa	Duodenum
45	chr1:76198600-76211600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:76198600-76212000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:76198800-76209400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:76198800-76210600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:76198800-76210800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:76199000-76207400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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