Variant report

Variant	rs9394371
Chromosome Location	chr6:36643755-36643756
allele	C/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	MTA3	chr6:36643664-36644402	GM12878	blood:	n/a	n/a
2	RUNX3	chr6:36643732-36644486	GM12878	blood:	n/a	n/a
3	STAT1	chr6:36643703-36644527	Hela-S3	cervix:	n/a	chr6:36643975-36643987 chr6:36643945-36643956
4	SPI1	chr6:36643745-36644175	GM12878	blood:	n/a	chr6:36644026-36644039 chr6:36643975-36643988 chr6:36643977-36643984 chr6:36643974-36643987
5	POLR2A	chr6:36643723-36644608	GM12892	blood:	n/a	n/a
6	MXI1	chr6:36643752-36648956	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr6:36643713-36644535	GM12892	blood:	n/a	n/a
8	MYBL2	chr6:36643703-36644625	HepG2	liver:	n/a	n/a
9	SPI1	chr6:36643706-36644247	HL-60	blood:	n/a	chr6:36644026-36644039 chr6:36643975-36643988 chr6:36643977-36643984 chr6:36643974-36643987
10	POLR2A	chr6:36643734-36644585	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:36643728-36644668	GM12891	blood:	n/a	n/a
12	SPI1	chr6:36643636-36644409	GM12878	blood:	n/a	chr6:36644026-36644039 chr6:36643975-36643988 chr6:36643977-36643984 chr6:36643974-36643987
13	HEY1	chr6:36643701-36644611	HepG2	liver:	n/a	n/a
14	WRNIP1	chr6:36643744-36644052	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:36643627-36647609	HepG2	liver:	n/a	n/a
16	FOXM1	chr6:36643653-36644408	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:36643719-36649046	GM12892	blood:	n/a	n/a
18	POLR2A	chr6:36643734-36644616	GM12892	blood:	n/a	n/a
19	NFIC	chr6:36643606-36644480	GM12878	blood:	n/a	n/a
20	POLR2A	chr6:36643740-36646846	HepG2	liver:	n/a	n/a
21	PML	chr6:36643564-36644638	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:36562081..36564755-chr6:36642636..36644724,2	K562	blood:
2	chr6:36581224..36597272-chr6:36642199..36659412,120	MCF-7	breast:
3	chr6:36559895..36571260-chr6:36642384..36648914,19	MCF-7	breast:
4	chr6:36581748..36603537-chr6:36641861..36652365,77	MCF-7	breast:

Variant related genes	Relation type
CDKN1A	TF binding region
ENSG00000263894	Chromatin interaction
ENSG00000112081	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1010423	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1010424	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10456441	0.84[ASN][1000 genomes]
rs10456442	0.84[ASN][1000 genomes]
rs10456443	0.84[ASN][1000 genomes]
rs10947616	0.82[ASN][1000 genomes]
rs10947618	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10947619	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10947620	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10947621	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10947622	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10947623	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11758192	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12174270	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12192827	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12192877	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12203953	0.81[ASN][1000 genomes]
rs12206430	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12210094	0.84[ASN][1000 genomes]
rs12214686	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12524435	0.82[ASN][1000 genomes]
rs12528913	0.83[ASN][1000 genomes]
rs12530170	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3829963	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3829965	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4464789	0.84[ASN][1000 genomes]
rs4711458	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4711459	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4711460	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4711461	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4711462	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4713993	0.82[ASN][1000 genomes]
rs4714002	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4714003	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58714705	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6457932	0.82[ASN][1000 genomes]
rs6457934	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6457935	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6920453	0.84[ASN][1000 genomes]
rs6931097	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72853320	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7382183	0.83[ASN][1000 genomes]
rs7747146	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9349002	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9349003	0.82[ASN][1000 genomes]
rs9349005	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9357222	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9366912	0.82[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	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36631000-36644000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:36635200-36643800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:36635400-36644000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:36635400-36645600	Weak transcription	Small Intestine	intestine
5	chr6:36635600-36644000	Weak transcription	Hela-S3	cervix
6	chr6:36636400-36643800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:36636400-36643800	Weak transcription	NH-A	brain
8	chr6:36637000-36643800	Weak transcription	Osteobl	bone
9	chr6:36637200-36643800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:36637200-36643800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:36637200-36643800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr6:36637200-36643800	Weak transcription	HSMM	muscle
13	chr6:36637800-36643800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:36637800-36643800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:36638800-36644200	Weak transcription	Ovary	ovary
16	chr6:36640000-36643800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:36640000-36643800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:36640000-36644000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr6:36640200-36643800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:36640400-36645600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr6:36640800-36643800	Weak transcription	Fetal Intestine Small	intestine
22	chr6:36641000-36643800	Weak transcription	Fetal Intestine Large	intestine
23	chr6:36641600-36643800	Enhancers	GM12878-XiMat	blood
24	chr6:36641800-36644000	Enhancers	Fetal Muscle Leg	muscle
25	chr6:36642200-36644000	Enhancers	HMEC	breast
26	chr6:36642400-36643800	Enhancers	NHEK	skin
27	chr6:36642400-36644000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:36642400-36646400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:36642600-36643800	Enhancers	HSMMtube	muscle
30	chr6:36642600-36644000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:36642800-36643800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:36643000-36644000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:36643400-36644000	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr6:36643400-36644000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:36643400-36644200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:36643400-36644800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr6:36643600-36643800	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr6:36643600-36644000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:36643600-36644000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:36643600-36644000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:36643600-36644000	Enhancers	Stomach Smooth Muscle	stomach
42	chr6:36643600-36644200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:36643600-36644200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:36643600-36644200	Flanking Active TSS	HepG2	liver
45	chr6:36643600-36644600	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr6:36643600-36644800	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr6:36643600-36646000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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