Variant report

Variant	rs4135239
Chromosome Location	chr6:36646353-36646354
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:435)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:435 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr6:36646144-36646677	K562	blood:	n/a	n/a
2	POLR2A	chr6:36646087-36648380	MCF-7	breast:	n/a	n/a
3	PAX5	chr6:36646169-36647164	GM12892	blood:	n/a	n/a
4	TBP	chr6:36646145-36646700	H1-hESC	embryonic stem cell:	n/a	n/a
5	NR3C1	chr6:36646066-36646634	ECC-1	luminal epithelium:	n/a	n/a
6	TAF1	chr6:36646339-36646653	GM12878	blood:	n/a	n/a
7	MAZ	chr6:36646010-36646676	K562	blood:	n/a	n/a
8	KAP1	chr6:36644788-36646792	HEK293	kidney:	n/a	n/a
9	TCF12	chr6:36645933-36647490	ECC-1	luminal epithelium:	n/a	chr6:36646343-36646350 chr6:36646484-36646491
10	NR3C1	chr6:36646136-36646582	ECC-1	luminal epithelium:	n/a	n/a
11	JUND	chr6:36646164-36646663	HepG2	liver:	n/a	n/a
12	HNF4A	chr6:36646103-36646641	HepG2	liver:	n/a	n/a
13	RELA	chr6:36646095-36646815	GM15510	blood:	n/a	n/a
14	POLR2A	chr6:36646191-36647159	A549	lung:	n/a	n/a
15	E2F6	chr6:36646069-36646779	H1-hESC	embryonic stem cell:	n/a	chr6:36646398-36646407
16	GTF2F1	chr6:36646073-36646873	Hela-S3	cervix:	n/a	n/a
17	GATA3	chr6:36645904-36647347	A549	lung:	n/a	n/a
18	NFIC	chr6:36645088-36646823	HepG2	liver:	n/a	n/a
19	MAX	chr6:36645923-36647461	A549	lung:	n/a	n/a
20	RAD21	chr6:36646002-36646833	ECC-1	luminal epithelium:	n/a	chr6:36646425-36646439
21	POLR2A	chr6:36646274-36648541	K562	blood:	n/a	n/a
22	MTA3	chr6:36646023-36647438	GM12878	blood:	n/a	n/a
23	SP1	chr6:36646047-36646711	HepG2	liver:	n/a	chr6:36646421-36646432 chr6:36646445-36646454 chr6:36646433-36646444 chr6:36646422-36646436 chr6:36646421-36646433
24	FOS	chr6:36646028-36646647	HUVEC	blood vessel:	n/a	n/a
25	RELA	chr6:36646219-36646733	GM12892	blood:	n/a	n/a
26	NFATC1	chr6:36645726-36649059	GM12878	blood:	n/a	n/a
27	TAF1	chr6:36646113-36646709	H1-hESC	embryonic stem cell:	n/a	n/a
28	MYC	chr6:36646212-36646786	MCF-7	breast:	n/a	n/a
29	FOXP2	chr6:36646317-36646592	SK-N-MC	brain:	n/a	n/a
30	TAF1	chr6:36646145-36647234	HepG2	liver:	n/a	n/a
31	CREB1	chr6:36646048-36646712	A549	lung:	n/a	n/a
32	PBX3	chr6:36646053-36648667	SK-N-SH	brain:	n/a	chr6:36646845-36646865
33	REST	chr6:36646095-36646696	HepG2	liver:	n/a	chr6:36646377-36646390
34	POLR2A	chr6:36646190-36646763	PFSK-1	brain:	n/a	n/a
35	HNF4A	chr6:36646206-36646635	HepG2	liver:	n/a	n/a
36	MAZ	chr6:36645377-36649066	IMR90	lung:	n/a	chr6:36648002-36648011
37	POLR2A	chr6:36646138-36646685	H1-hESC	embryonic stem cell:	n/a	n/a
38	MAX	chr6:36645983-36646993	SK-N-SH	brain:	n/a	n/a
39	ZBTB7A	chr6:36646155-36646495	HepG2	liver:	n/a	n/a
40	TCF7L2	chr6:36646269-36647316	HCT-116	colon:	n/a	chr6:36647211-36647220
41	NFIC	chr6:36646046-36647416	SK-N-SH	brain:	n/a	n/a
42	SIN3AK20	chr6:36645970-36647256	MCF-7	breast:	n/a	n/a
43	WRNIP1	chr6:36645250-36647385	GM12878	blood:	n/a	n/a
44	TBL1XR1	chr6:36646332-36646529	K562	blood:	n/a	n/a
45	POLR2A	chr6:36646141-36648422	GM10847	blood:	n/a	n/a
46	ZKSCAN1	chr6:36646143-36647381	Hela-S3	cervix:	n/a	n/a
47	RCOR1	chr6:36646074-36647424	Hela-S3	cervix:	n/a	n/a
48	BHLHE40	chr6:36646076-36647353	K562	blood:	n/a	n/a
49	EP300	chr6:36645336-36646668	HepG2	liver:	n/a	n/a
50	EP300	chr6:36645859-36647516	ECC-1	luminal epithelium:	n/a	chr6:36646808-36646824

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36645391..36647920-chr6:36680659..36684331,3	MCF-7	breast:
2	chr6:36589971..36596625-chr6:36645571..36650576,10	K562	blood:
3	chr17:57914670..57916833-chr6:36645394..36647964,3	MCF-7	breast:
4	chr6:36644838..36653438-chr6:36718524..36730954,23	MCF-7	breast:
5	chr1:40042208..40042835-chr6:36646343..36646854,2	HCT-116	colon:
6	chr6:36644040..36648031-chr6:36680924..36685784,5	MCF-7	breast:
7	chr17:56707748..56709290-chr6:36645821..36647810,2	MCF-7	breast:
8	chr6:36581224..36597272-chr6:36642199..36659412,120	MCF-7	breast:
9	chr6:36560711..36564837-chr6:36645733..36649715,9	K562	blood:
10	chr6:36560285..36563984-chr6:36645642..36649715,8	K562	blood:
11	chr6:36559895..36571260-chr6:36642384..36648914,19	MCF-7	breast:
12	chr6:36606453..36608701-chr6:36645452..36648033,2	MCF-7	breast:
13	chr6:36645102..36656546-chr6:36717974..36730993,29	MCF-7	breast:
14	chr6:36589213..36595227-chr6:36645571..36651666,9	K562	blood:
15	chr6:36560169..36564521-chr6:36645252..36648947,8	MCF-7	breast:
16	chr6:36581748..36603537-chr6:36641861..36652365,77	MCF-7	breast:

No data

Variant related genes	Relation type
CDKN1A	TF binding region
ENSG00000124772	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000090621	Chromatin interaction
ENSG00000255587	Chromatin interaction
ENSG00000112081	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000238554	Chromatin interaction
ENSG00000263894	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1321312	0.93[ASN][1000 genomes]
rs1969701	0.93[ASN][1000 genomes]
rs1977172	0.93[ASN][1000 genomes]
rs3176330	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3176331	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3829966	1.00[ASN][1000 genomes]
rs3829967	1.00[ASN][1000 genomes]
rs3829968	0.97[ASN][1000 genomes]
rs4135234	0.99[ASN][1000 genomes]
rs4135237	1.00[ASN][1000 genomes]
rs4713997	0.93[ASN][1000 genomes]
rs4714000	0.97[ASN][1000 genomes]
rs6457936	0.97[ASN][1000 genomes]
rs6902994	0.84[ASN][1000 genomes]
rs6907801	0.93[ASN][1000 genomes]
rs6926780	0.93[ASN][1000 genomes]
rs7452626	0.97[ASN][1000 genomes]
rs762623	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380585	0.93[ASN][1000 genomes]
rs9380586	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv885807	chr6:36645696-36651889	Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36642400-36646400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:36643800-36646400	Bivalent Enhancer	Fetal Thymus	thymus
3	chr6:36643800-36646400	Enhancers	Pancreas	Pancrea
4	chr6:36643800-36646400	Enhancers	Stomach Mucosa	stomach
5	chr6:36643800-36646400	Flanking Active TSS	NHEK	skin
6	chr6:36644000-36646400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:36644000-36646400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:36644000-36646400	Enhancers	Placenta	Placenta
9	chr6:36644000-36646400	Enhancers	Lung	lung
10	chr6:36644000-36646400	Flanking Active TSS	HMEC	breast
11	chr6:36644200-36647600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:36644400-36646400	Weak transcription	Spleen	Spleen
13	chr6:36644800-36646400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
14	chr6:36644800-36646400	Flanking Active TSS	GM12878-XiMat	blood
15	chr6:36645000-36646400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:36645000-36646400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:36645000-36646600	Enhancers	Fetal Heart	heart
18	chr6:36645200-36646400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:36645400-36646400	Enhancers	Primary T cells fromperipheralblood	blood
20	chr6:36645400-36646400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr6:36645400-36646600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:36645600-36646400	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:36645600-36646400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr6:36645600-36646400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr6:36645600-36646400	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr6:36645600-36646400	Flanking Active TSS	Fetal Intestine Large	intestine
27	chr6:36645600-36646400	Flanking Active TSS	Fetal Intestine Small	intestine
28	chr6:36645600-36646400	Bivalent Enhancer	Fetal Stomach	stomach
29	chr6:36645600-36646400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:36645600-36646400	Enhancers	Small Intestine	intestine
31	chr6:36645600-36646400	Flanking Active TSS	HepG2	liver
32	chr6:36645600-36646400	Flanking Active TSS	NHLF	lung
33	chr6:36645600-36647000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr6:36645600-36648600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr6:36645800-36646800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:36645800-36647400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr6:36646000-36646400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
38	chr6:36646000-36646400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
39	chr6:36646000-36646400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:36646000-36646400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
41	chr6:36646000-36646400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:36646000-36646400	Flanking Active TSS	Brain Substantia Nigra	brain
43	chr6:36646000-36646400	Flanking Active TSS	Fetal Muscle Trunk	muscle
44	chr6:36646000-36646400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
45	chr6:36646000-36646400	Enhancers	Left Ventricle	heart
46	chr6:36646000-36646400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr6:36646000-36646400	Flanking Active TSS	NH-A	brain
48	chr6:36646000-36646600	Enhancers	Primary hematopoietic stem cells	blood
49	chr6:36646000-36646600	Bivalent/Poised TSS	Fetal Brain Female	brain
50	chr6:36646000-36646600	Active TSS	Stomach Smooth Muscle	stomach

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