Variant report

Variant	rs6509927
Chromosome Location	chr19:55678225-55678226
allele	A/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	CREB1	chr19:55677212-55678393	A549	lung:	n/a	n/a
2	EP300	chr19:55678066-55678536	K562	blood:	n/a	chr19:55678279-55678293 chr19:55678161-55678170 chr19:55678398-55678414
3	JUND	chr19:55678093-55678497	H1-hESC	embryonic stem cell:	n/a	chr19:55678397-55678406 chr19:55678251-55678263
4	NR2F2	chr19:55677218-55678548	K562	blood:	n/a	n/a
5	BHLHE40	chr19:55678156-55678528	GM12878	blood:	n/a	n/a
6	CTCF	chr19:55678220-55678370	AG04449	skin:	n/a	n/a
7	CREB1	chr19:55677273-55678376	H1-hESC	embryonic stem cell:	n/a	n/a
8	RCOR1	chr19:55677348-55679357	Hela-S3	cervix:	n/a	n/a
9	FOXA1	chr19:55678100-55678513	ECC-1	luminal epithelium:	n/a	n/a
10	MXI1	chr19:55677412-55678666	Hela-S3	cervix:	n/a	chr19:55678148-55678163 chr19:55678146-55678161
11	HCFC1	chr19:55677117-55678511	K562	blood:	n/a	n/a
12	JUND	chr19:55678005-55678535	A549	lung:	n/a	chr19:55678397-55678406 chr19:55678085-55678094 chr19:55678251-55678263 chr19:55678044-55678053
13	SP4	chr19:55677806-55678555	H1-hESC	embryonic stem cell:	n/a	chr19:55678197-55678208 chr19:55678172-55678188 chr19:55678176-55678187
14	HA-E2F1	chr19:55678091-55678975	MCF-7	breast:	n/a	chr19:55678165-55678174
15	USF2	chr19:55677391-55678669	Hela-S3	cervix:	n/a	chr19:55677560-55677576
16	REST	chr19:55678155-55678623	A549	lung:	n/a	chr19:55678398-55678408
17	CEBPZ	chr19:55677943-55678401	HepG2	liver:	n/a	n/a
18	CHD2	chr19:55677306-55678568	Hela-S3	cervix:	n/a	chr19:55678401-55678411
19	MAX	chr19:55677959-55678562	H1-hESC	embryonic stem cell:	n/a	n/a
20	CHD2	chr19:55677925-55678234	HepG2	liver:	n/a	n/a
21	ELK1	chr19:55677402-55678648	Hela-S3	cervix:	n/a	n/a
22	CCNT2	chr19:55677243-55678286	K562	blood:	n/a	n/a
23	BRCA1	chr19:55678039-55678495	HepG2	liver:	n/a	n/a
24	IRF3	chr19:55677961-55678245	GM12878	blood:	n/a	chr19:55678176-55678190
25	TCF7L2	chr19:55677370-55678721	HCT-116	colon:	n/a	n/a
26	JUND	chr19:55678087-55678500	H1-hESC	embryonic stem cell:	n/a	chr19:55678397-55678406 chr19:55678251-55678263
27	MAX	chr19:55677266-55678748	A549	lung:	n/a	n/a
28	JUND	chr19:55677340-55678600	H1-hESC	embryonic stem cell:	n/a	chr19:55677826-55677835 chr19:55678397-55678406 chr19:55678085-55678094 chr19:55677821-55677830 chr19:55678251-55678263 chr19:55678044-55678053
29	NRF1	chr19:55677983-55678760	Hela-S3	cervix:	n/a	chr19:55678577-55678588
30	POLR2A	chr19:55677743-55678902	SK-N-MC	brain:	n/a	n/a
31	RUNX3	chr19:55677891-55678283	GM12878	blood:	n/a	n/a
32	YY1	chr19:55677417-55678242	K562	blood:	n/a	n/a
33	MAX	chr19:55677114-55678906	A549	lung:	n/a	n/a
34	MYC	chr19:55677369-55678569	K562	blood:	n/a	n/a
35	SIN3A	chr19:55677187-55678671	H1-hESC	embryonic stem cell:	n/a	chr19:55677563-55677574 chr19:55677543-55677556
36	CEBPB	chr19:55678107-55678906	A549	lung:	n/a	chr19:55678315-55678332
37	FOS	chr19:55677894-55678286	Hela-S3	cervix:	n/a	chr19:55678085-55678094 chr19:55678251-55678263 chr19:55678044-55678053
38	TCF7L2	chr19:55678198-55678623	HEK293	kidney:	n/a	n/a
39	ZMIZ1	chr19:55677937-55678473	K562	blood:	n/a	n/a
40	SP1	chr19:55677194-55678829	A549	lung:	n/a	chr19:55678402-55678411 chr19:55678402-55678411 chr19:55677857-55677864 chr19:55678197-55678208 chr19:55678041-55678062 chr19:55678082-55678103 chr19:55678403-55678412 chr19:55678176-55678187 chr19:55677824-55677838
41	NRF1	chr19:55677945-55678876	SK-N-SH	brain:	n/a	chr19:55678577-55678588
42	SREBP1	chr19:55677482-55678490	HepG2	liver:	n/a	chr19:55678147-55678161 chr19:55678148-55678162
43	TCF12	chr19:55677159-55678932	A549	lung:	n/a	n/a
44	SREBP1	chr19:55677827-55678813	GM12878	blood:	n/a	chr19:55678147-55678161 chr19:55678148-55678162
45	SIX5	chr19:55678051-55678527	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr19:55677892-55678265	HCT-116	colon:	n/a	n/a
47	RCOR1	chr19:55677944-55678633	K562	blood:	n/a	n/a
48	SMARCC1	chr19:55677169-55678418	Hela-S3	cervix:	n/a	chr19:55677445-55677454
49	SIN3AK20	chr19:55677254-55678584	PANC-1	pancreas:	n/a	n/a
50	SP1	chr19:55677808-55678600	H1-hESC	embryonic stem cell:	n/a	chr19:55678402-55678411 chr19:55678402-55678411 chr19:55677857-55677864 chr19:55678197-55678208 chr19:55678041-55678062 chr19:55678082-55678103 chr19:55678403-55678412 chr19:55678176-55678187 chr19:55677824-55677838

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:55678215-55678265	HepG2	liver:	n/a
2	chr19:55678215-55678265	NB4	blood:	n/a
3	chr19:55678215-55678265	HEK293	kidney:	embryo
4	chr19:55678215-55678265	T-47D	breast:	n/a
5	chr19:55678215-55678265	GM06990	blood:	n/a
6	chr19:55678215-55678265	Jurkat	blood:	n/a
7	chr19:55678215-55678265	AG09309	skin:	n/a
8	chr19:55678215-55678265	CMK	blood:	n/a
9	chr19:55678215-55678265	Hepatocyte	liver:	n/a
10	chr19:55678215-55678265	HRCEpiC	kidney:	n/a
11	chr19:55678215-55678265	HCT-116	colon:	n/a
12	chr19:55678215-55678265	HCF	heart:	n/a
13	chr19:55678215-55678265	IMR90	lung:	fetal
14	chr19:55678215-55678265	NHBE	bronchial:	n/a
15	chr19:55678215-55678265	HAEpiC	amniotic membrane:	n/a
16	chr19:55678215-55678265	PFSK-1	brain:	n/a
17	chr19:55678215-55678265	AG09319	gingival:	n/a
18	chr19:55678215-55678265	SAEC	small airway:	n/a
19	chr19:55678215-55678265	HRE	kidney:	n/a
20	chr19:55678215-55678265	Caco-2	colon:	n/a
21	chr19:55678215-55678265	HPAEpiC	pulmonary alveolar:	n/a
22	chr19:55678215-55678265	HNPCEpiC	eye:	n/a
23	chr19:55678215-55678265	SK-N-MC	brain:	n/a
24	chr19:55678215-55678265	GM12891	blood:	n/a
25	chr19:55678215-55678265	PANC-1	pancreas:	n/a
26	chr19:55678215-55678265	K562	blood:	n/a
27	chr19:55678215-55678265	SK-N-SH	brain:	n/a
28	chr19:55678215-55678265	AG04449	skin:	fetal
29	chr19:55678215-55678265	PrEC	prostate:	n/a
30	chr19:55678215-55678265	HUVEC	blood vessel:	n/a
31	chr19:55678215-55678265	Hela-S3	cervix:	n/a
32	chr19:55678215-55678265	GM12892	blood:	n/a
33	chr19:55678215-55678265	HCPEpiC	choroid plexus:	n/a
34	chr19:55678215-55678265	NH-A	brain:	n/a
35	chr19:55678215-55678265	NHDF-neo	bronchial:	n/a
36	chr19:55678215-55678265	U87	brain:	n/a
37	chr19:55678215-55678265	H1-hESC	embryonic stem cell:	embryo
38	chr19:55678215-55678265	AG04450	lung:	fetal
39	chr19:55678215-55678265	ECC-1	luminal epithelium:	n/a
40	chr19:55678215-55678265	BE2_C	brain:	n/a
41	chr19:55678215-55678265	A549	lung:	n/a
42	chr19:55678215-55678265	HRPEpiC	eye:	n/a
43	chr19:55678215-55678265	HIPEpiC	eye:	n/a
44	chr19:55678215-55678265	SK-N-SH_RA	brain:	n/a
45	chr19:55678215-55678265	HEEpiC	esophagus:	n/a
46	chr19:55678215-55678265	BJ	skin:	n/a
47	chr19:55678215-55678265	GM19239	blood:	n/a
48	chr19:55678215-55678265	AoSMC	blood vessel:	n/a
49	chr19:55678215-55678265	MCF-7	breast:	n/a
50	chr19:55678215-55678265	HL-60	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:55676623..55678727-chr19:55917591..55919258,2	MCF-7	breast:
2	chr19:55669094..55672573-chr19:55676633..55678240,3	K562	blood:
3	chr19:55677411..55679148-chr19:55895317..55896952,2	MCF-7	breast:
4	chr19:55677572..55679137-chr19:55970708..55972707,2	K562	blood:
5	chr19:55676191..55679387-chr19:55917452..55919839,3	K562	blood:
6	chr19:55676374..55679520-chr19:55726674..55730754,4	K562	blood:
7	chr19:55592134..55595044-chr19:55674815..55678963,4	K562	blood:
8	chr19:55666873..55668722-chr19:55676430..55678695,2	K562	blood:
9	chr19:55672196..55674741-chr19:55676544..55679173,3	K562	blood:
10	chr19:55677235..55679036-chr19:55897209..55898733,2	K562	blood:
11	chr19:55677803..55679380-chr19:55684043..55686956,2	MCF-7	breast:
12	chr19:55677887..55680823-chr19:55918139..55920221,3	K562	blood:
13	chr19:55590129..55594149-chr19:55677127..55678963,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPS8L1-2	chr19:55677187-55678229	NONHSAT067999

Variant related genes	Relation type
DNAAF3	TF binding region
ENSG00000239137	TF binding region
ENSG00000239137	CpG island
DNAAF3	CpG island
ENSG00000267577	Chromatin interaction
ENSG00000129991	Chromatin interaction
ENSG00000167646	Chromatin interaction
ENSG00000131037	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000267649	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000267110	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000108107	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10424609	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10424638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11669300	0.88[ASN][1000 genomes]
rs11670538	0.96[ASN][1000 genomes]
rs11672000	0.88[ASN][1000 genomes]
rs11672834	0.88[ASN][1000 genomes]
rs12104158	0.85[AFR][1000 genomes]
rs13343638	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16986289	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16986292	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16986294	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3729837	1.00[ASN][1000 genomes]
rs3729841	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs3859540	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.96[LWK][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3859542	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7248799	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107129	0.96[ASN][1000 genomes]
rs8107736	0.96[ASN][1000 genomes]
rs8110415	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9749340	0.96[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	nsv534462	chr19:55028722-55683018	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv912451	chr19:55595687-55680746	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv912453	chr19:55672007-55690398	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6509927	ZNF552	cis	parietal	SCAN
rs6509927	ZNF324	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55677000-55678400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr19:55677200-55678400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:55677200-55678400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr19:55677200-55678400	Active TSS	Brain Anterior Caudate	brain
5	chr19:55677200-55678400	Bivalent/Poised TSS	Colonic Mucosa	Colon
6	chr19:55677200-55678400	Active TSS	HSMM	muscle
7	chr19:55677200-55678600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr19:55677200-55678600	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr19:55677200-55678600	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr19:55677200-55678600	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr19:55677200-55678600	Active TSS	Muscle Satellite Cultured Cells	--
12	chr19:55677200-55678800	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr19:55677200-55678800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
14	chr19:55677200-55679000	Enhancers	Spleen	Spleen
15	chr19:55677200-55679200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr19:55677400-55678400	Active TSS	H1 Cell Line	embryonic stem cell
17	chr19:55677400-55678400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:55677400-55678400	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr19:55677400-55678400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:55677400-55678400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:55677400-55678400	Weak transcription	Fetal Heart	heart
22	chr19:55677400-55678400	Active TSS	HepG2	liver
23	chr19:55677400-55678400	Active TSS	HSMMtube	muscle
24	chr19:55677400-55678400	Active TSS	K562	blood
25	chr19:55677400-55678600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:55677400-55678600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
27	chr19:55677400-55678800	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr19:55677400-55678800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr19:55677400-55678800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
30	chr19:55677400-55678800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr19:55677400-55678800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
32	chr19:55677400-55678800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
33	chr19:55677400-55678800	Active TSS	Fetal Kidney	kidney
34	chr19:55677400-55678800	Active TSS	NHDF-Ad	bronchial
35	chr19:55677400-55679000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
36	chr19:55677400-55679000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
37	chr19:55677400-55679000	Active TSS	A549	lung
38	chr19:55677400-55679200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
39	chr19:55677600-55678600	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr19:55677600-55678600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr19:55677600-55678600	Active TSS	Fetal Intestine Small	intestine
42	chr19:55677600-55678600	Active TSS	Psoas Muscle	Psoas
43	chr19:55677600-55678600	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
44	chr19:55677600-55678600	Active TSS	Right Atrium	heart
45	chr19:55677600-55678600	Bivalent/Poised TSS	Stomach Mucosa	stomach
46	chr19:55677600-55678600	Enhancers	GM12878-XiMat	blood
47	chr19:55677600-55678800	Active TSS	H9 Cell Line	embryonic stem cell
48	chr19:55677600-55678800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr19:55677600-55678800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr19:55677600-55678800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--

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