Variant report

Variant	rs2395655
Chromosome Location	chr6:36645696-36645697
allele	A/G
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	STAT3	chr6:36645054-36646335	MCF10A-Er-Src	breast:	n/a	chr6:36645802-36645822 chr6:36645808-36645817 chr6:36645808-36645816 chr6:36645802-36645822 chr6:36645807-36645816
2	RUNX3	chr6:36644763-36645901	GM12878	blood:	n/a	n/a
3	KAP1	chr6:36644788-36646792	HEK293	kidney:	n/a	n/a
4	NFIC	chr6:36645088-36646823	HepG2	liver:	n/a	n/a
5	POLR2A	chr6:36645492-36645775	HepG2	liver:	n/a	n/a
6	SP1	chr6:36645479-36646038	HepG2	liver:	n/a	n/a
7	FOXA1	chr6:36645399-36646046	HepG2	liver:	n/a	n/a
8	ELF1	chr6:36645458-36645987	HepG2	liver:	n/a	chr6:36645809-36645818
9	MAZ	chr6:36645377-36649066	IMR90	lung:	n/a	chr6:36648002-36648011
10	TBP	chr6:36645416-36645915	HepG2	liver:	n/a	n/a
11	WRNIP1	chr6:36645250-36647385	GM12878	blood:	n/a	n/a
12	EP300	chr6:36645336-36646668	HepG2	liver:	n/a	n/a
13	HEY1	chr6:36644699-36647538	HepG2	liver:	n/a	chr6:36646439-36646454 chr6:36646399-36646414
14	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
15	ZEB1	chr6:36644713-36647578	HepG2	liver:	n/a	n/a
16	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
17	RELA	chr6:36645476-36646918	GM19099	blood:	n/a	n/a
18	E2F6	chr6:36645672-36647088	A549	lung:	n/a	chr6:36646398-36646407
19	ARID3A	chr6:36645573-36646745	HepG2	liver:	n/a	n/a
20	MXI1	chr6:36643959-36649033	IMR90	lung:	n/a	n/a
21	POLR2A	chr6:36643939-36647410	HepG2	liver:	n/a	n/a
22	SRF	chr6:36645666-36645829	GM12878	blood:	n/a	chr6:36645773-36645791 chr6:36645774-36645791
23	POLR2A	chr6:36644766-36648199	MCF10A-Er-Src	breast:	n/a	n/a
24	TEAD4	chr6:36645211-36646668	HepG2	liver:	n/a	n/a
25	POLR2A	chr6:36644776-36645864	GM19193	blood:	n/a	n/a
26	PML	chr6:36644718-36649008	GM12878	blood:	n/a	chr6:36648003-36648012
27	POLR2A	chr6:36644702-36645953	GM12892	blood:	n/a	n/a
28	POLR2A	chr6:36645352-36648955	HepG2	liver:	n/a	n/a
29	MAFF	chr6:36645587-36645902	HepG2	liver:	n/a	n/a
30	SRF	chr6:36645579-36645964	HepG2	liver:	n/a	chr6:36645773-36645791 chr6:36645774-36645791
31	POLR2A	chr6:36645411-36645734	GM12891	blood:	n/a	n/a
32	MAX	chr6:36643823-36648608	HepG2	liver:	n/a	chr6:36648002-36648011
33	FOS	chr6:36645641-36645783	MCF10A-Er-Src	breast:	n/a	n/a
34	SRF	chr6:36645485-36646045	ECC-1	luminal epithelium:	n/a	chr6:36645773-36645791 chr6:36645774-36645791
35	POLR2A	chr6:36644830-36649007	GM12878	blood:	n/a	n/a
36	RELA	chr6:36645060-36646770	GM12891	blood:	n/a	n/a
37	SRF	chr6:36645472-36646774	ECC-1	luminal epithelium:	n/a	chr6:36645773-36645791 chr6:36645774-36645791
38	USF2	chr6:36645625-36645880	HepG2	liver:	n/a	chr6:36645815-36645826
39	SMC3	chr6:36645532-36645735	HepG2	liver:	n/a	n/a
40	POLR2A	chr6:36644736-36646047	HepG2	liver:	n/a	n/a
41	NFYB	chr6:36645625-36645825	GM12878	blood:	n/a	n/a
42	RAD21	chr6:36645559-36645763	HepG2	liver:	n/a	n/a
43	MXI1	chr6:36643752-36648956	SK-N-SH	brain:	n/a	n/a
44	POLR2A	chr6:36645402-36645962	HepG2	liver:	n/a	n/a
45	SRF	chr6:36645666-36645877	GM12878	blood:	n/a	chr6:36645773-36645791 chr6:36645774-36645791
46	HDAC2	chr6:36645531-36646841	HepG2	liver:	n/a	n/a
47	POLR2A	chr6:36644081-36649028	IMR90	lung:	n/a	n/a
48	POLR2A	chr6:36644870-36645864	HepG2	liver:	n/a	n/a
49	MYBL2	chr6:36644928-36647408	HepG2	liver:	n/a	n/a
50	SRF	chr6:36645457-36645973	HepG2	liver:	n/a	chr6:36645773-36645791 chr6:36645774-36645791

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:36645648-36645698	U87	brain:	n/a
2	chr6:36645648-36645698	AG04449	skin:	fetal
3	chr6:36645648-36645698	ovcar-3	ovarian:	n/a
4	chr6:36645648-36645698	MCF10A-Er-Src	breast:	n/a
5	chr6:36645648-36645698	NHDF-neo	bronchial:	n/a
6	chr6:36645648-36645698	BE2_C	brain:	n/a
7	chr6:36645648-36645698	Caco-2	colon:	n/a
8	chr6:36645648-36645698	HRPEpiC	eye:	n/a
9	chr6:36645648-36645698	HEEpiC	esophagus:	n/a
10	chr6:36645648-36645698	GM06990	blood:	n/a
11	chr6:36645648-36645698	HCT-116	colon:	n/a
12	chr6:36645648-36645698	SAEC	small airway:	n/a
13	chr6:36645648-36645698	PFSK-1	brain:	n/a
14	chr6:36645648-36645698	GM12891	blood:	n/a
15	chr6:36645648-36645698	Hepatocyte	liver:	n/a
16	chr6:36645648-36645698	HMEC	breast:	n/a
17	chr6:36645648-36645698	AG10803	skin:	n/a
18	chr6:36645648-36645698	LNCaP	prostate:	n/a
19	chr6:36645648-36645698	RPTEC	kidney:	n/a
20	chr6:36645648-36645698	HCM	heart:	n/a
21	chr6:36645648-36645698	GM19239	blood:	n/a
22	chr6:36645648-36645698	HCPEpiC	choroid plexus:	n/a
23	chr6:36645648-36645698	CMK	blood:	n/a
24	chr6:36645648-36645698	BJ	skin:	n/a
25	chr6:36645648-36645698	SK-N-SH	brain:	n/a
26	chr6:36645648-36645698	PrEC	prostate:	n/a
27	chr6:36645648-36645698	AG04450	lung:	fetal
28	chr6:36645648-36645698	NT2-D1	testis:	n/a
29	chr6:36645648-36645698	NB4	blood:	n/a
30	chr6:36645648-36645698	HepG2	liver:	n/a
31	chr6:36645648-36645698	HNPCEpiC	eye:	n/a
32	chr6:36645648-36645698	SK-N-SH_RA	brain:	n/a
33	chr6:36645648-36645698	HRCEpiC	kidney:	n/a
34	chr6:36645648-36645698	MCF-7	breast:	n/a
35	chr6:36645648-36645698	NH-A	brain:	n/a
36	chr6:36645648-36645698	HUVEC	blood vessel:	n/a
37	chr6:36645648-36645698	AG09319	gingival:	n/a
38	chr6:36645648-36645698	AoSMC	blood vessel:	n/a
39	chr6:36645648-36645698	ProgFib	skin:	n/a
40	chr6:36645648-36645698	GM12892	blood:	n/a
41	chr6:36645648-36645698	T-47D	breast:	n/a
42	chr6:36645648-36645698	HIPEpiC	eye:	n/a
43	chr6:36645648-36645698	Jurkat	blood:	n/a
44	chr6:36645648-36645698	ECC-1	luminal epithelium:	n/a
45	chr6:36645648-36645698	HEK293	kidney:	embryo
46	chr6:36645648-36645698	K562	blood:	n/a
47	chr6:36645648-36645698	GM12878	blood:	n/a
48	chr6:36645648-36645698	HL-60	blood:	n/a
49	chr6:36645648-36645698	PANC-1	pancreas:	n/a
50	chr6:36645648-36645698	SKMC	muscle:	n/a

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	chr6:36644040..36648031-chr6:36680924..36685784,5	MCF-7	breast:
6	chr6:36581224..36597272-chr6:36642199..36659412,120	MCF-7	breast:
7	chr6:36560285..36563984-chr6:36645642..36649715,8	K562	blood:
8	chr6:36559895..36571260-chr6:36642384..36648914,19	MCF-7	breast:
9	chr6:36606453..36608701-chr6:36645452..36648033,2	MCF-7	breast:
10	chr6:36645102..36656546-chr6:36717974..36730993,29	MCF-7	breast:
11	chr6:36589213..36595227-chr6:36645571..36651666,9	K562	blood:
12	chr6:36560169..36564521-chr6:36645252..36648947,8	MCF-7	breast:
13	chr6:36581748..36603537-chr6:36641861..36652365,77	MCF-7	breast:

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

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10807170	0.86[MEX][hapmap]
rs1321308	0.81[GIH][hapmap]
rs3176320	0.96[CEU][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3176323	0.88[CEU][hapmap];0.86[MEX][hapmap]
rs3176334	0.92[CEU][hapmap]
rs3176336	0.81[EUR][1000 genomes]
rs4711457	0.81[MEX][hapmap]
rs4713999	0.81[MEX][hapmap]
rs4714001	0.82[AMR][1000 genomes]
rs733590	0.84[CEU][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes];0.81[EUR][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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2395655	CDKN1A	cis	Lymphoblastoid	GTEx
rs2395655		cis	Lymphoblastoid	GTEx
rs2395655	CDKN1A	cis	multi-tissue	Pritchard
rs2395655	SNRPC	cis	cerebellum	SCAN
rs2395655	PI16	cis	parietal	SCAN

Chromatin state (count:111 , 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	chr6:36643600-36646000	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr6:36643800-36645800	Enhancers	HUVEC	blood vessel
4	chr6:36643800-36646000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:36643800-36646000	Enhancers	Brain Substantia Nigra	brain
6	chr6:36643800-36646000	Enhancers	NH-A	brain
7	chr6:36643800-36646200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:36643800-36646200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:36643800-36646400	Bivalent Enhancer	Fetal Thymus	thymus
10	chr6:36643800-36646400	Enhancers	Pancreas	Pancrea
11	chr6:36643800-36646400	Enhancers	Stomach Mucosa	stomach
12	chr6:36643800-36646400	Flanking Active TSS	NHEK	skin
13	chr6:36644000-36646000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:36644000-36646000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:36644000-36646000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:36644000-36646000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:36644000-36646000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:36644000-36646000	Enhancers	Brain Anterior Caudate	brain
19	chr6:36644000-36646000	Enhancers	Colonic Mucosa	Colon
20	chr6:36644000-36646000	Bivalent Enhancer	Fetal Muscle Leg	muscle
21	chr6:36644000-36646200	Enhancers	Esophagus	oesophagus
22	chr6:36644000-36646200	Flanking Active TSS	HSMM	muscle
23	chr6:36644000-36646400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:36644000-36646400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:36644000-36646400	Enhancers	Placenta	Placenta
26	chr6:36644000-36646400	Enhancers	Lung	lung
27	chr6:36644000-36646400	Flanking Active TSS	HMEC	breast
28	chr6:36644200-36646000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:36644200-36646200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:36644200-36647600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:36644400-36646000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
32	chr6:36644400-36646000	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr6:36644400-36646400	Weak transcription	Spleen	Spleen
34	chr6:36644600-36645800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
35	chr6:36644600-36645800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
36	chr6:36644600-36646000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
37	chr6:36644800-36645800	Enhancers	Aorta	Aorta
38	chr6:36644800-36646000	Enhancers	Liver	Liver
39	chr6:36644800-36646000	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr6:36644800-36646200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:36644800-36646200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr6:36644800-36646200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:36644800-36646200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:36644800-36646200	Flanking Active TSS	HSMMtube	muscle
45	chr6:36644800-36646400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
46	chr6:36644800-36646400	Flanking Active TSS	GM12878-XiMat	blood
47	chr6:36645000-36646000	Enhancers	Brain Hippocampus Middle	brain
48	chr6:36645000-36646200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
49	chr6:36645000-36646200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:36645000-36646200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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