Variant report

Variant	rs7247677
Chromosome Location	chr19:56187097-56187098
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	SIN3AK20	chr19:56186054-56187433	PANC-1	pancreas:	n/a	n/a
2	MAX	chr19:56186163-56187127	A549	lung:	n/a	n/a
3	MAZ	chr19:56185625-56187879	IMR90	lung:	n/a	n/a
4	MXI1	chr19:56186291-56187173	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr19:56186232-56187185	Raji	blood:	n/a	n/a
6	GABPA	chr19:56185875-56187128	K562	blood:	n/a	chr19:56186319-56186328 chr19:56186566-56186573 chr19:56186868-56186877
7	SREBP2	chr19:56186088-56187387	GM12878	blood:	n/a	n/a
8	TBL1XR1	chr19:56186970-56187215	K562	blood:	n/a	n/a
9	GABPA	chr19:56186180-56187190	MCF-7	breast:	n/a	chr19:56186319-56186328 chr19:56186566-56186573 chr19:56186868-56186877
10	POLR2A	chr19:56185595-56187287	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:56185967-56187116	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr19:56186257-56187520	IMR90	lung:	n/a	n/a
13	POLR2A	chr19:56185589-56187693	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr19:56185658-56187111	Hela-S3	cervix:	n/a	n/a
15	STAT5A	chr19:56186154-56187213	GM12878	blood:	n/a	chr19:56186620-56186632
16	HA-E2F1	chr19:56186301-56187273	MCF-7	breast:	n/a	chr19:56186653-56186662
17	HCFC1	chr19:56185639-56187350	Hela-S3	cervix:	n/a	n/a
18	MAFK	chr19:56187030-56187472	IMR90	lung:	n/a	n/a
19	SIN3AK20	chr19:56186204-56187133	K562	blood:	n/a	n/a
20	RCOR1	chr19:56186324-56187195	K562	blood:	n/a	n/a
21	POLR2A	chr19:56185652-56187179	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr19:56185613-56187158	GM12891	blood:	n/a	n/a
23	POLR2A	chr19:56185739-56187205	A549	lung:	n/a	n/a
24	POLR2A	chr19:56185507-56187227	GM12878	blood:	n/a	n/a
25	POLR2A	chr19:56185664-56187793	PANC-1	pancreas:	n/a	n/a
26	GABPA	chr19:56185814-56187449	A549	lung:	n/a	chr19:56186319-56186328 chr19:56186566-56186573 chr19:56186868-56186877
27	POLR2A	chr19:56186200-56187102	GM19099	blood:	n/a	n/a
28	POLR2A	chr19:56186827-56187195	GM12891	blood:	n/a	n/a
29	POLR2A	chr19:56185622-56187312	K562	blood:	n/a	n/a
30	MAX	chr19:56186291-56187183	NB4	blood:	n/a	n/a
31	POLR2A	chr19:56185621-56187334	HepG2	liver:	n/a	n/a
32	POLR2A	chr19:56185523-56187118	K562	blood:	n/a	n/a
33	TBL1XR1	chr19:56186401-56187279	K562	blood:	n/a	n/a
34	POLR2A	chr19:56186077-56187260	HUVEC	blood vessel:	n/a	n/a
35	MAX	chr19:56186208-56187116	SK-N-SH	brain:	n/a	n/a
36	MAX	chr19:56186350-56187246	GM12878	blood:	n/a	n/a
37	STAT1	chr19:56187070-56187104	GM12878	blood:	n/a	n/a
38	MAFK	chr19:56187002-56187333	HepG2	liver:	n/a	n/a
39	POLR2A	chr19:56186821-56187284	U87	brain:	n/a	n/a
40	POLR2A	chr19:56185570-56187206	GM12892	blood:	n/a	n/a
41	POLR2A	chr19:56186190-56187215	GM12878	blood:	n/a	n/a
42	POLR2A	chr19:56186049-56187140	GM12878	blood:	n/a	n/a
43	POLR2A	chr19:56185761-56187676	GM12891	blood:	n/a	n/a
44	MXI1	chr19:56186051-56187291	IMR90	lung:	n/a	n/a
45	MXI1	chr19:56185791-56188335	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr19:56185988-56187218	GM18505	blood:	n/a	n/a
47	BCL3	chr19:56186092-56187354	A549	lung:	n/a	chr19:56186662-56186671 chr19:56186569-56186578 chr19:56186659-56186668 chr19:56186810-56186819 chr19:56186433-56186442 chr19:56186182-56186195 chr19:56186420-56186433 chr19:56186475-56186484 chr19:56186189-56186202 chr19:56186657-56186670 chr19:56187225-56187234
48	POLR2A	chr19:56187084-56187463	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr19:56186176-56187101	H1-neurons	neurons:	n/a	n/a
50	CHD2	chr19:56186239-56187133	Hela-S3	cervix:	n/a	chr19:56186637-56186647

No.	Distal block	Cell Line	Cell type
1	chr19:56164666..56171824-chr19:56183341..56192911,16	MCF-7	breast:
2	chr19:56185642..56190165-chr19:56193908..56196750,4	MCF-7	breast:
3	chr19:56152964..56155802-chr19:56186387..56188533,2	MCF-7	breast:
4	chr19:56114907..56116947-chr19:56184542..56187154,2	K562	blood:
5	chr19:55918601..55920426-chr19:56186578..56189029,2	K562	blood:
6	chr19:56158129..56161096-chr19:56185326..56187791,3	MCF-7	breast:

Variant related genes	Relation type
EPN1	TF binding region
ENSG00000267523	TF binding region
ENSG00000108106	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000173581	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000211571	Chromatin interaction
ENSG00000063244	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1808393	0.83[ASN][1000 genomes]
rs2864434	0.83[ASN][1000 genomes]
rs310436	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4801265	0.81[CHB][hapmap]
rs485152	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs504850	0.95[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs519856	0.86[ASN][1000 genomes]
rs579496	0.81[ASN][1000 genomes]
rs596075	0.81[ASN][1000 genomes]
rs643368	0.83[ASN][1000 genomes]
rs664684	0.86[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7249837	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7252055	0.84[ASN][1000 genomes]
rs8791	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs889092	0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	nsv522559	chr19:56185250-56190815	Strong transcription Flanking Active TSS Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7247677	ZNF256	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56185200-56187600	Active TSS	H9 Cell Line	embryonic stem cell
2	chr19:56185200-56187800	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr19:56185400-56187400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr19:56185400-56187400	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr19:56185400-56187400	Active TSS	K562	blood
6	chr19:56185400-56188000	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr19:56185400-56188000	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr19:56185600-56187600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr19:56185600-56187600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr19:56185600-56188000	Active TSS	HSMM	muscle
11	chr19:56185800-56187200	Active TSS	H1 Cell Line	embryonic stem cell
12	chr19:56185800-56187400	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr19:56185800-56187400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:56185800-56187600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr19:56185800-56187800	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr19:56185800-56187800	Active TSS	Psoas Muscle	Psoas
17	chr19:56185800-56187800	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr19:56186000-56187200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr19:56186000-56187200	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr19:56186000-56187200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr19:56186000-56187200	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr19:56186000-56187200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:56186000-56187200	Active TSS	Brain Substantia Nigra	brain
24	chr19:56186000-56187200	Active TSS	Colon Smooth Muscle	Colon
25	chr19:56186000-56187200	Active TSS	Placenta	Placenta
26	chr19:56186000-56187200	Active TSS	Fetal Stomach	stomach
27	chr19:56186000-56187200	Active TSS	Fetal Thymus	thymus
28	chr19:56186000-56187200	Active TSS	Osteobl	bone
29	chr19:56186000-56187400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:56186000-56187400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:56186000-56187400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr19:56186000-56187400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:56186000-56187400	Active TSS	Muscle Satellite Cultured Cells	--
34	chr19:56186000-56187400	Active TSS	Fetal Kidney	kidney
35	chr19:56186000-56187400	Active TSS	Ovary	ovary
36	chr19:56186000-56187400	Active TSS	HMEC	breast
37	chr19:56186000-56187400	Active TSS	HSMMtube	muscle
38	chr19:56186000-56187400	Active TSS	NH-A	brain
39	chr19:56186000-56187600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr19:56186000-56187600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:56186000-56187600	Active TSS	Stomach Mucosa	stomach
42	chr19:56186000-56187600	Active TSS	A549	lung
43	chr19:56186000-56187800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr19:56186000-56187800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr19:56186000-56187800	Active TSS	NHLF	lung
46	chr19:56186000-56188000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr19:56186000-56188000	Active TSS	GM12878-XiMat	blood
48	chr19:56186000-56188000	Active TSS	NHDF-Ad	bronchial
49	chr19:56186200-56187200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr19:56186200-56187200	Active TSS	Breast Myoepithelial Primary Cells	Breast

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