Variant report

Variant	rs2180860
Chromosome Location	chr6:119257137-119257138
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:12)
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	CBX3	chr6:119257135-119257978	K562	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:119257082..119259694-chr6:119259960..119261722,2	K562	blood:
2	chr6:119213694..119219544-chr6:119251621..119258172,21	K562	blood:
3	chr6:119256349..119258481-chr6:119264695..119266812,2	K562	blood:
4	chr6:119256205..119257932-chr6:119293855..119296677,2	K562	blood:
5	chr6:119213036..119217484-chr6:119254311..119257675,9	MCF-7	breast:
6	chr6:119242613..119249110-chr6:119251513..119257145,6	MCF-7	breast:
7	chr6:119256106..119257947-chr6:119468580..119471034,2	K562	blood:
8	chr6:119255727..119258203-chr6:119400226..119402388,2	K562	blood:
9	chr6:119214552..119219906-chr6:119253918..119257622,8	MCF-7	breast:
10	chr6:119253238..119258280-chr6:119398045..119402661,8	K562	blood:
11	chr6:119256460..119259122-chr6:119259921..119263121,4	K562	blood:
12	chr6:119213105..119220728-chr6:119253299..119257962,22	K562	blood:

No data

Variant related genes	Relation type
MCM9	TF binding region
ENSG00000111879	Chromatin interaction
ENSG00000111875	Chromatin interaction
ENSG00000111877	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1022706	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1022707	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1022708	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1022709	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10499090	0.82[ASN][1000 genomes]
rs11153782	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11965951	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11967231	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11967232	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12527291	0.91[ASN][1000 genomes]
rs12527363	0.82[ASN][1000 genomes]
rs1807979	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1885125	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2145569	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2145570	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35906538	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3756940	0.82[ASN][1000 genomes]
rs3945959	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245502	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4946367	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4946369	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4946370	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4946371	0.98[ASN][1000 genomes]
rs4946372	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4946373	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4946374	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4946376	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4946377	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4946378	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4946380	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4946381	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4946382	0.90[ASN][1000 genomes]
rs4946385	0.85[ASN][1000 genomes]
rs4946386	0.82[ASN][1000 genomes]
rs55978448	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56022752	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62422265	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62422266	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62422267	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62422268	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62422269	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62422270	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6569035	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6901738	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6903220	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6903579	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6904381	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6910377	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6910782	0.83[EUR][1000 genomes]
rs6916168	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6916291	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6916491	0.96[ASN][1000 genomes]
rs6916672	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6918569	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6918844	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6919100	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6923637	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6923771	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6928315	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6928945	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6931423	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6933970	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6935960	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6939937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6940120	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72970476	0.82[ASN][1000 genomes]
rs7381533	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7381535	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7381546	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7741149	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7758729	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7758849	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7758862	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7759423	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9320669	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9320670	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9320671	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9372517	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9374759	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9374763	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9374764	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9374765	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9374766	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9374767	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9385060	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9385063	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9387610	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9387611	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9387612	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9387613	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9387621	0.91[ASN][1000 genomes]
rs9401099	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9401103	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9401106	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9489563	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9489569	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9689589	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs988098	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9968863	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv16596	chr6:119251007-119272087	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
2	nsv437523	chr6:119251971-119260280	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2180860	MCM9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119254000-119257400	Active TSS	GM12878-XiMat	blood
2	chr6:119255000-119257200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:119255000-119257200	Active TSS	Stomach Smooth Muscle	stomach
4	chr6:119255200-119257200	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr6:119255200-119257400	Active TSS	HSMM	muscle
6	chr6:119255400-119257200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:119255400-119257400	Active TSS	Hela-S3	cervix
8	chr6:119255600-119257200	Active TSS	Osteobl	bone
9	chr6:119255600-119257600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:119256400-119257200	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr6:119256400-119257200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:119256600-119257200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:119256600-119257200	Weak transcription	Lung	lung
14	chr6:119256600-119257200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr6:119256600-119257800	Flanking Active TSS	Dnd41	blood
16	chr6:119256600-119258000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:119256600-119260800	Weak transcription	Esophagus	oesophagus
18	chr6:119256600-119260800	Weak transcription	Left Ventricle	heart
19	chr6:119256600-119261800	Weak transcription	Gastric	stomach
20	chr6:119256600-119262000	Weak transcription	Pancreas	Pancrea
21	chr6:119256800-119257200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr6:119256800-119257200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:119256800-119257200	Enhancers	Liver	Liver
24	chr6:119256800-119257200	Enhancers	Brain Anterior Caudate	brain
25	chr6:119256800-119257200	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr6:119256800-119257200	Enhancers	Fetal Heart	heart
27	chr6:119256800-119257200	Weak transcription	Placenta	Placenta
28	chr6:119256800-119257200	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr6:119256800-119257400	Enhancers	Primary B cells from cord blood	blood
30	chr6:119256800-119257400	Enhancers	Brain Hippocampus Middle	brain
31	chr6:119256800-119257600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:119256800-119257800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:119256800-119258400	Enhancers	Primary B cells from peripheral blood	blood
34	chr6:119256800-119260800	Weak transcription	Fetal Stomach	stomach
35	chr6:119256800-119260800	Weak transcription	Right Ventricle	heart
36	chr6:119256800-119261000	Weak transcription	Aorta	Aorta
37	chr6:119256800-119262000	Weak transcription	Thymus	Thymus
38	chr6:119257000-119257200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr6:119257000-119257200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:119257000-119257200	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr6:119257000-119257200	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr6:119257000-119257200	Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr6:119257000-119257200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr6:119257000-119257200	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr6:119257000-119257200	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr6:119257000-119257200	Enhancers	Brain Cingulate Gyrus	brain
47	chr6:119257000-119257200	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr6:119257000-119257200	Enhancers	Fetal Kidney	kidney
49	chr6:119257000-119257200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr6:119257000-119257200	Enhancers	Rectal Smooth Muscle	rectum

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