Variant report

Variant	rs3829966
Chromosome Location	chr6:36644951-36644952
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	RUNX3	chr6:36644763-36645901	GM12878	blood:	n/a	n/a
2	KAP1	chr6:36644788-36646792	HEK293	kidney:	n/a	n/a
3	HEY1	chr6:36644699-36647538	HepG2	liver:	n/a	chr6:36646439-36646454 chr6:36646399-36646414
4	RAD21	chr6:36643874-36649108	SK-N-SH	brain:	n/a	chr6:36644187-36644201 chr6:36646425-36646439 chr6:36646938-36646951 chr6:36647756-36647766 chr6:36644031-36644045
5	POLR2A	chr6:36644720-36645332	GM12892	blood:	n/a	n/a
6	ZEB1	chr6:36644713-36647578	HepG2	liver:	n/a	n/a
7	CTCF	chr6:36644920-36645070	HPF	lung:	n/a	n/a
8	CTCF	chr6:36644682-36649046	SK-N-SH	brain:	n/a	chr6:36644843-36644861 chr6:36647784-36647797 chr6:36646423-36646441 chr6:36645963-36645970 chr6:36647827-36647836 chr6:36647770-36647780
9	POLR2A	chr6:36644771-36645118	HepG2	liver:	n/a	n/a
10	POLR2A	chr6:36644755-36645214	HepG2	liver:	n/a	n/a
11	MXI1	chr6:36643959-36649033	IMR90	lung:	n/a	n/a
12	POLR2A	chr6:36643939-36647410	HepG2	liver:	n/a	n/a
13	POLR2A	chr6:36644766-36648199	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr6:36644776-36645864	GM19193	blood:	n/a	n/a
15	PML	chr6:36644718-36649008	GM12878	blood:	n/a	chr6:36648003-36648012
16	POLR2A	chr6:36644702-36645953	GM12892	blood:	n/a	n/a
17	POLR2A	chr6:36644846-36645354	GM12878	blood:	n/a	n/a
18	MAX	chr6:36643823-36648608	HepG2	liver:	n/a	chr6:36648002-36648011
19	POLR2A	chr6:36644830-36649007	GM12878	blood:	n/a	n/a
20	POLR2A	chr6:36644736-36646047	HepG2	liver:	n/a	n/a
21	MXI1	chr6:36643752-36648956	SK-N-SH	brain:	n/a	n/a
22	TAF1	chr6:36644951-36645216	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr6:36644081-36649028	IMR90	lung:	n/a	n/a
24	POLR2A	chr6:36644870-36645864	HepG2	liver:	n/a	n/a
25	MYBL2	chr6:36644928-36647408	HepG2	liver:	n/a	n/a
26	CTCF	chr6:36644840-36644990	GM12873	blood:	n/a	chr6:36644843-36644861
27	POLR2A	chr6:36644855-36645258	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr6:36644752-36645245	GM12891	blood:	n/a	n/a
29	POLR2A	chr6:36644651-36645314	GM12891	blood:	n/a	n/a
30	NFIC	chr6:36644925-36646697	HepG2	liver:	n/a	n/a
31	MYBL2	chr6:36643933-36646660	HepG2	liver:	n/a	n/a
32	POLR2A	chr6:36643627-36647609	HepG2	liver:	n/a	n/a
33	STAT5A	chr6:36644796-36645214	GM12878	blood:	n/a	n/a
34	HEY1	chr6:36644712-36645339	HepG2	liver:	n/a	n/a
35	REST	chr6:36644931-36645350	MCF-7	breast:	n/a	n/a
36	POLR2A	chr6:36643787-36657761	GM12891	blood:	n/a	n/a
37	KAP1	chr6:36644053-36645893	U2OS	brain:	n/a	n/a
38	POLR2A	chr6:36644775-36645312	GM12878	blood:	n/a	n/a
39	TBP	chr6:36644005-36645127	HepG2	liver:	n/a	n/a
40	POLR2A	chr6:36643814-36656801	GM12878	blood:	n/a	n/a
41	MBD4	chr6:36643803-36647135	HepG2	liver:	n/a	n/a
42	MAX	chr6:36643809-36647379	HepG2	liver:	n/a	n/a
43	POLR2A	chr6:36644718-36649084	GM12891	blood:	n/a	n/a
44	POLR2A	chr6:36644815-36649061	GM12878	blood:	n/a	n/a
45	ZNF143	chr6:36644879-36645204	GM12878	blood:	n/a	n/a
46	POLR2A	chr6:36643719-36649046	GM12892	blood:	n/a	n/a
47	ZNF263	chr6:36643938-36645253	HEK293-T-REx	kidney:	n/a	n/a
48	POLR2A	chr6:36644706-36645969	GM12878	blood:	n/a	n/a
49	POLR2A	chr6:36644779-36645160	GM12878	blood:	n/a	n/a
50	MTA3	chr6:36644644-36649073	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:36644838..36653438-chr6:36718524..36730954,23	MCF-7	breast:
2	chr6:36644040..36648031-chr6:36680924..36685784,5	MCF-7	breast:
3	chr6:36581224..36597272-chr6:36642199..36659412,120	MCF-7	breast:
4	chr6:36559895..36571260-chr6:36642384..36648914,19	MCF-7	breast:
5	chr6:36581748..36603537-chr6:36641861..36652365,77	MCF-7	breast:

Variant related genes	Relation type
CDKN1A	TF binding region
ENSG00000263894	Chromatin interaction
ENSG00000255587	Chromatin interaction
ENSG00000124772	Chromatin interaction
ENSG00000112081	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1321312	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1969701	0.93[ASN][1000 genomes]
rs1977172	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3176330	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3176331	0.92[ASN][1000 genomes]
rs3829967	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3829968	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4135234	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4135237	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4135239	1.00[ASN][1000 genomes]
rs4713997	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4714000	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6457936	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6902994	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6907801	0.93[ASN][1000 genomes]
rs6926780	0.93[ASN][1000 genomes]
rs7452626	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs762623	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9380585	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9380586	0.81[AMR][1000 genomes];0.93[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:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36635400-36645600	Weak transcription	Small Intestine	intestine
2	chr6:36640400-36645600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:36642400-36646400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:36643600-36646000	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr6:36643800-36645000	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr6:36643800-36645400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:36643800-36645400	Enhancers	NHDF-Ad	bronchial
8	chr6:36643800-36645600	Enhancers	Adipose Nuclei	Adipose
9	chr6:36643800-36645600	Enhancers	Brain Angular Gyrus	brain
10	chr6:36643800-36645600	Enhancers	Fetal Intestine Large	intestine
11	chr6:36643800-36645600	Enhancers	Fetal Intestine Small	intestine
12	chr6:36643800-36645600	Enhancers	A549	lung
13	chr6:36643800-36645600	Enhancers	NHLF	lung
14	chr6:36643800-36645600	Enhancers	Osteobl	bone
15	chr6:36643800-36645800	Enhancers	HUVEC	blood vessel
16	chr6:36643800-36646000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:36643800-36646000	Enhancers	Brain Substantia Nigra	brain
18	chr6:36643800-36646000	Enhancers	NH-A	brain
19	chr6:36643800-36646200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:36643800-36646200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:36643800-36646400	Bivalent Enhancer	Fetal Thymus	thymus
22	chr6:36643800-36646400	Enhancers	Pancreas	Pancrea
23	chr6:36643800-36646400	Enhancers	Stomach Mucosa	stomach
24	chr6:36643800-36646400	Flanking Active TSS	NHEK	skin
25	chr6:36644000-36645000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:36644000-36645400	Enhancers	Muscle Satellite Cultured Cells	--
27	chr6:36644000-36645400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr6:36644000-36645400	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr6:36644000-36645600	Enhancers	Duodenum Mucosa	Duodenum
30	chr6:36644000-36645600	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr6:36644000-36645600	Enhancers	Hela-S3	cervix
32	chr6:36644000-36646000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:36644000-36646000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:36644000-36646000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr6:36644000-36646000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:36644000-36646000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr6:36644000-36646000	Enhancers	Brain Anterior Caudate	brain
38	chr6:36644000-36646000	Enhancers	Colonic Mucosa	Colon
39	chr6:36644000-36646000	Bivalent Enhancer	Fetal Muscle Leg	muscle
40	chr6:36644000-36646200	Enhancers	Esophagus	oesophagus
41	chr6:36644000-36646200	Flanking Active TSS	HSMM	muscle
42	chr6:36644000-36646400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:36644000-36646400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:36644000-36646400	Enhancers	Placenta	Placenta
45	chr6:36644000-36646400	Enhancers	Lung	lung
46	chr6:36644000-36646400	Flanking Active TSS	HMEC	breast
47	chr6:36644200-36645000	Enhancers	Ovary	ovary
48	chr6:36644200-36645000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr6:36644200-36645600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr6:36644200-36645600	Flanking Bivalent TSS/Enh	HepG2	liver

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