Variant report

Variant	rs6800307
Chromosome Location	chr3:145970425-145970426
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr3:145970319-145970604	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:145970385-145970435	MCF-7	breast:	n/a
2	chr3:145970385-145970435	A549	lung:	n/a
3	chr3:145970385-145970435	HAEpiC	amniotic membrane:	n/a
4	chr3:145970385-145970435	SK-N-MC	brain:	n/a
5	chr3:145970385-145970435	PFSK-1	brain:	n/a
6	chr3:145970385-145970435	RPTEC	kidney:	n/a
7	chr3:145970385-145970435	HNPCEpiC	eye:	n/a
8	chr3:145970385-145970435	LNCaP	prostate:	n/a
9	chr3:145970385-145970435	Hepatocyte	liver:	n/a
10	chr3:145970385-145970435	GM12891	blood:	n/a
11	chr3:145970385-145970435	PrEC	prostate:	n/a
12	chr3:145970385-145970435	NT2-D1	testis:	n/a
13	chr3:145970385-145970435	AG10803	skin:	n/a
14	chr3:145970385-145970435	U87	brain:	n/a
15	chr3:145970385-145970435	HL-60	blood:	n/a
16	chr3:145970385-145970435	HEEpiC	esophagus:	n/a
17	chr3:145970385-145970435	SK-N-SH	brain:	n/a
18	chr3:145970385-145970435	HRCEpiC	kidney:	n/a
19	chr3:145970385-145970435	IMR90	lung:	fetal
20	chr3:145970385-145970435	HUVEC	blood vessel:	n/a
21	chr3:145970385-145970435	HEK293	kidney:	embryo
22	chr3:145970385-145970435	AG09319	gingival:	n/a
23	chr3:145970385-145970435	ovcar-3	ovarian:	n/a
24	chr3:145970385-145970435	HRPEpiC	eye:	n/a
25	chr3:145970385-145970435	AoSMC	blood vessel:	n/a
26	chr3:145970385-145970435	HCPEpiC	choroid plexus:	n/a
27	chr3:145970385-145970435	GM12892	blood:	n/a
28	chr3:145970385-145970435	NH-A	brain:	n/a
29	chr3:145970385-145970435	BE2_C	brain:	n/a
30	chr3:145970385-145970435	HPAEpiC	pulmonary alveolar:	n/a
31	chr3:145970385-145970435	HCF	heart:	n/a
32	chr3:145970385-145970435	SAEC	small airway:	n/a
33	chr3:145970385-145970435	HRE	kidney:	n/a
34	chr3:145970385-145970435	SKMC	muscle:	n/a
35	chr3:145970385-145970435	SK-N-SH_RA	brain:	n/a
36	chr3:145970385-145970435	ProgFib	skin:	n/a
37	chr3:145970385-145970435	AG04450	lung:	fetal
38	chr3:145970385-145970435	HMEC	breast:	n/a
39	chr3:145970385-145970435	H1-hESC	embryonic stem cell:	embryo
40	chr3:145970385-145970435	Jurkat	blood:	n/a
41	chr3:145970385-145970435	HIPEpiC	eye:	n/a
42	chr3:145970385-145970435	HCM	heart:	n/a
43	chr3:145970385-145970435	AG09309	skin:	n/a
44	chr3:145970385-145970435	PANC-1	pancreas:	n/a
45	chr3:145970385-145970435	T-47D	breast:	n/a
46	chr3:145970385-145970435	Caco-2	colon:	n/a
47	chr3:145970385-145970435	Hela-S3	cervix:	n/a
48	chr3:145970385-145970435	HCT-116	colon:	n/a
49	chr3:145970385-145970435	AG04449	skin:	fetal
50	chr3:145970385-145970435	GM12878	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:145878599..145881384-chr3:145968449..145970595,2	MCF-7	breast:

No data

Variant related genes	Relation type
PLSCR4	TF binding region
PLSCR4	CpG island
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10222588	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10737947	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10804710	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10935611	0.83[ASN][1000 genomes]
rs10935613	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10935614	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10935615	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10935616	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11709096	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11716310	0.82[ASN][1000 genomes]
rs11915448	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11919011	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11926517	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12632757	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12633074	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1355570	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1398125	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1398529	0.83[ASN][1000 genomes]
rs1512078	0.88[ASN][1000 genomes]
rs1512079	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1512081	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1512888	0.82[ASN][1000 genomes]
rs1512890	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1828560	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1877511	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1913184	0.82[ASN][1000 genomes]
rs2036980	0.82[ASN][1000 genomes]
rs2175544	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2175545	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2867081	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2867083	0.88[ASN][1000 genomes]
rs2867084	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2903478	0.82[ASN][1000 genomes]
rs2903479	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3762686	0.82[ASN][1000 genomes]
rs3762688	0.82[ASN][1000 genomes]
rs3792338	0.82[ASN][1000 genomes]
rs3804648	0.82[ASN][1000 genomes]
rs3804654	0.82[ASN][1000 genomes]
rs3914252	0.82[ASN][1000 genomes]
rs4273339	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4475004	0.81[ASN][1000 genomes]
rs4488802	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4610193	0.91[ASN][1000 genomes]
rs4681306	0.88[ASN][1000 genomes]
rs4681307	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4681308	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4681310	0.91[ASN][1000 genomes]
rs6440421	0.83[ASN][1000 genomes]
rs6440422	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6770163	0.83[ASN][1000 genomes]
rs6770278	0.83[ASN][1000 genomes]
rs6775520	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792732	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6805377	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7430290	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7612683	0.82[ASN][1000 genomes]
rs7621841	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7632412	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7634568	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7643778	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7645100	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs907490	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs925464	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9756128	0.82[ASN][1000 genomes]
rs9809892	0.82[ASN][1000 genomes]
rs9813122	0.88[ASN][1000 genomes]
rs9822280	0.82[ASN][1000 genomes]
rs9825776	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9826132	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9826360	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9838801	0.83[ASN][1000 genomes]
rs9838866	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9839724	0.82[ASN][1000 genomes]
rs9839874	0.82[ASN][1000 genomes]
rs9845890	0.88[ASN][1000 genomes]
rs9850566	0.82[ASN][1000 genomes]
rs9851511	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9855695	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9858823	0.81[ASN][1000 genomes]
rs9859273	0.81[ASN][1000 genomes]
rs9863647	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9867851	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9875799	0.89[ASN][1000 genomes]
rs9877004	0.82[ASN][1000 genomes]
rs9881755	0.84[AMR][1000 genomes];0.91[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	nsv877614	chr3:145903426-146025896	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv877615	chr3:145910430-145988231	ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv877616	chr3:145921954-145983688	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv3333601	chr3:145940702-146068210	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv3416330	chr3:145941029-146068457	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3452197	chr3:145950303-145974111	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	esv3333990	chr3:145950303-145982133	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv998388	chr3:145960954-146087749	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145969200-145974600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:145969200-145974800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:145970200-145971400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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