Variant report

Variant	rs7255531
Chromosome Location	chr19:56215439-56215440
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	POLR2A	chr19:56215233-56215481	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr19:56214994-56215470	A549	lung:	n/a	n/a
3	MAX	chr19:56214933-56215714	H1-hESC	embryonic stem cell:	n/a	chr19:56215523-56215534 chr19:56215523-56215534 chr19:56215526-56215542 chr19:56215524-56215533
4	CTCF	chr19:56215072-56215456	K562	blood:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
5	TBP	chr19:56215255-56215455	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr19:56214975-56215539	HCT-116	colon:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
7	POLR2A	chr19:56214997-56220979	K562	blood:	n/a	n/a
8	E2F6	chr19:56214942-56215596	H1-hESC	embryonic stem cell:	n/a	n/a
9	CCNT2	chr19:56215133-56215480	K562	blood:	n/a	n/a
10	POLR2A	chr19:56215209-56215456	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr19:56215052-56215448	HepG2	liver:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
12	MAX	chr19:56214993-56215667	H1-hESC	embryonic stem cell:	n/a	chr19:56215523-56215534 chr19:56215523-56215534 chr19:56215526-56215542 chr19:56215524-56215533
13	ZNF143	chr19:56215082-56215452	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr19:56215340-56215490	AG04450	lung:	n/a	n/a
15	CTCF	chr19:56215300-56215450	HCM	heart:	n/a	n/a
16	ZBTB33	chr19:56215035-56215448	K562	blood:	n/a	n/a
17	CTCF	chr19:56214932-56215610	A549	lung:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
18	POLR2A	chr19:56215251-56215491	H1-hESC	embryonic stem cell:	n/a	n/a
19	RAD21	chr19:56215126-56215450	H1-hESC	embryonic stem cell:	n/a	chr19:56215255-56215269 chr19:56215254-56215273 chr19:56215259-56215271 chr19:56215257-56215270
20	MAX	chr19:56214994-56215449	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr19:56215098-56215525	K562	blood:	n/a	n/a
22	POLR2A	chr19:56215137-56215594	HepG2	liver:	n/a	n/a
23	POLR2A	chr19:56215160-56217154	SK-N-MC	brain:	n/a	n/a
24	RAD21	chr19:56214983-56215499	H1-hESC	embryonic stem cell:	n/a	chr19:56215255-56215269 chr19:56215254-56215273 chr19:56215259-56215271 chr19:56215257-56215270
25	POLR2A	chr19:56215148-56215632	GM12878	blood:	n/a	n/a
26	TEAD4	chr19:56215030-56215451	K562	blood:	n/a	n/a
27	CTCF	chr19:56215061-56215564	K562	blood:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
28	RAD21	chr19:56215096-56215458	H1-hESC	embryonic stem cell:	n/a	chr19:56215255-56215269 chr19:56215254-56215273 chr19:56215259-56215271 chr19:56215257-56215270
29	MAX	chr19:56214949-56215528	K562	blood:	n/a	n/a
30	CTCF	chr19:56215068-56215466	MCF-7	breast:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
31	CTCF	chr19:56214933-56215607	SK-N-SH	brain:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
32	CTCF	chr19:56215018-56215471	H1-hESC	embryonic stem cell:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
33	RAD21	chr19:56214938-56215581	HCT-116	colon:	n/a	chr19:56215255-56215269 chr19:56215254-56215273 chr19:56215517-56215529 chr19:56215259-56215271 chr19:56215257-56215270
34	POLR2A	chr19:56214868-56217148	PANC-1	pancreas:	n/a	n/a
35	BHLHE40	chr19:56215071-56215519	K562	blood:	n/a	n/a
36	E2F6	chr19:56214913-56216027	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr19:56215183-56215644	GM12878	blood:	n/a	n/a
38	ELF1	chr19:56215150-56215495	GM12878	blood:	n/a	n/a
39	GTF2F1	chr19:56215023-56215476	H1-hESC	embryonic stem cell:	n/a	n/a
40	TEAD4	chr19:56215182-56215453	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:56215426-56215476	NHBE	bronchial:	n/a
2	chr19:56215426-56215476	HIPEpiC	eye:	n/a
3	chr19:56215426-56215476	BE2_C	brain:	n/a
4	chr19:56215426-56215476	K562	blood:	n/a
5	chr19:56215426-56215476	ProgFib	skin:	n/a
6	chr19:56215426-56215476	HCPEpiC	choroid plexus:	n/a
7	chr19:56215426-56215476	U87	brain:	n/a
8	chr19:56215426-56215476	SAEC	small airway:	n/a
9	chr19:56215426-56215476	GM19239	blood:	n/a
10	chr19:56215426-56215476	HEK293	kidney:	embryo
11	chr19:56215426-56215476	HL-60	blood:	n/a
12	chr19:56215426-56215476	AG09309	skin:	n/a
13	chr19:56215426-56215476	AG09319	gingival:	n/a
14	chr19:56215426-56215476	NHDF-neo	bronchial:	n/a
15	chr19:56215426-56215476	AG04450	lung:	fetal
16	chr19:56215426-56215476	GM06990	blood:	n/a
17	chr19:56215426-56215476	ovcar-3	ovarian:	n/a
18	chr19:56215426-56215476	HRE	kidney:	n/a
19	chr19:56215426-56215476	HCM	heart:	n/a
20	chr19:56215426-56215476	AoSMC	blood vessel:	n/a
21	chr19:56215426-56215476	Jurkat	blood:	n/a
22	chr19:56215426-56215476	HRCEpiC	kidney:	n/a
23	chr19:56215426-56215476	Hepatocyte	liver:	n/a
24	chr19:56215426-56215476	HMEC	breast:	n/a
25	chr19:56215426-56215476	SKMC	muscle:	n/a
26	chr19:56215426-56215476	NB4	blood:	n/a
27	chr19:56215426-56215476	NT2-D1	testis:	n/a
28	chr19:56215426-56215476	Caco-2	colon:	n/a
29	chr19:56215426-56215476	HUVEC	blood vessel:	n/a
30	chr19:56215426-56215476	MCF10A-Er-Src	breast:	n/a
31	chr19:56215426-56215476	ECC-1	luminal epithelium:	n/a
32	chr19:56215426-56215476	LNCaP	prostate:	n/a
33	chr19:56215426-56215476	HCT-116	colon:	n/a
34	chr19:56215426-56215476	RPTEC	kidney:	n/a
35	chr19:56215426-56215476	SK-N-SH	brain:	n/a
36	chr19:56215426-56215476	HCF	heart:	n/a
37	chr19:56215426-56215476	SK-N-SH_RA	brain:	n/a
38	chr19:56215426-56215476	PFSK-1	brain:	n/a
39	chr19:56215426-56215476	MCF-7	breast:	n/a
40	chr19:56215426-56215476	H1-hESC	embryonic stem cell:	embryo
41	chr19:56215426-56215476	A549	lung:	n/a
42	chr19:56215426-56215476	PANC-1	pancreas:	n/a
43	chr19:56215426-56215476	GM12892	blood:	n/a
44	chr19:56215426-56215476	AG04449	skin:	fetal
45	chr19:56215426-56215476	SK-N-MC	brain:	n/a
46	chr19:56215426-56215476	HAEpiC	amniotic membrane:	n/a
47	chr19:56215426-56215476	NH-A	brain:	n/a
48	chr19:56215426-56215476	GM12878	blood:	n/a
49	chr19:56215426-56215476	PrEC	prostate:	n/a
50	chr19:56215426-56215476	HNPCEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56185419..56191490-chr19:56212273..56216664,6	K562	blood:
2	chr19:56214734..56218976-chr19:56219559..56224015,5	K562	blood:

Variant related genes	Relation type
ENSG00000267865	TF binding region
ENSG00000268593	TF binding region
ENSG00000268593	CpG island
ENSG00000267865	CpG island
ENSG00000267865	Chromatin interaction
ENSG00000267523	Chromatin interaction
ENSG00000063245	Chromatin interaction
ENSG00000269574	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2287831	1.00[ASW][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap]
rs2287832	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34637812	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35562577	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7247619	0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
2	nsv833882	chr19:56158633-56326564	Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv1061024	chr19:56167101-56217359	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1057383	chr19:56211031-56456028	ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7255531	ZNF580	cis	lymphoblastoid	seeQTL
rs7255531	ZNF256	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56188200-56218200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:56188600-56215600	Weak transcription	Fetal Brain Male	brain
3	chr19:56191800-56218800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr19:56195400-56217600	Weak transcription	Right Atrium	heart
5	chr19:56200000-56216000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr19:56202600-56217000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:56206600-56218600	Weak transcription	HepG2	liver
8	chr19:56207000-56219200	Weak transcription	Psoas Muscle	Psoas
9	chr19:56207400-56215800	Weak transcription	HSMMtube	muscle
10	chr19:56207600-56216600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:56207800-56216800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:56208000-56220000	Weak transcription	Fetal Lung	lung
13	chr19:56208200-56215800	Weak transcription	Primary B cells from cord blood	blood
14	chr19:56208400-56215800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr19:56209000-56217800	Weak transcription	Hela-S3	cervix
16	chr19:56209000-56218000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr19:56209200-56215800	Weak transcription	Osteobl	bone
18	chr19:56209400-56218200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr19:56210000-56217800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr19:56210000-56217800	Weak transcription	Brain Hippocampus Middle	brain
21	chr19:56210000-56218000	Weak transcription	Left Ventricle	heart
22	chr19:56210000-56218400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr19:56210000-56219600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr19:56210000-56220000	Weak transcription	Fetal Brain Female	brain
25	chr19:56210200-56216000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr19:56211200-56218000	Weak transcription	NHEK	skin
27	chr19:56211200-56220800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr19:56212400-56215600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr19:56212400-56215800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr19:56212400-56215800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:56212400-56215800	Weak transcription	Colonic Mucosa	Colon
32	chr19:56212400-56215800	Weak transcription	GM12878-XiMat	blood
33	chr19:56212400-56217400	Weak transcription	Thymus	Thymus
34	chr19:56212400-56217600	Weak transcription	Aorta	Aorta
35	chr19:56212400-56217600	Weak transcription	Fetal Muscle Leg	muscle
36	chr19:56212400-56217800	Weak transcription	Brain Germinal Matrix	brain
37	chr19:56212400-56218000	Weak transcription	Brain Anterior Caudate	brain
38	chr19:56212400-56218200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr19:56212400-56218200	Weak transcription	HMEC	breast
40	chr19:56212400-56218400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr19:56212400-56218400	Weak transcription	Liver	Liver
42	chr19:56212400-56218800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr19:56212400-56219200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:56212400-56224000	Weak transcription	HSMM	muscle
45	chr19:56212600-56215600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr19:56212600-56215800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr19:56212600-56215800	Weak transcription	Lung	lung
48	chr19:56212600-56216200	Weak transcription	Esophagus	oesophagus
49	chr19:56212600-56217600	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr19:56212600-56218400	Weak transcription	Stomach Smooth Muscle	stomach

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