Variant report

Variant	rs1319075
Chromosome Location	chr6:28662521-28662522
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28622745..28624261-chr6:28661466..28664275,2	K562	blood:
2	chr6:28660970..28662889-chr6:28669119..28670853,2	K562	blood:
3	chr6:28660878..28662982-chr6:28701014..28703051,2	K562	blood:
4	chr6:28659445..28664236-chr6:28674743..28678587,5	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12180700	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12211927	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1337585	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1810619	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2394149	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs370520	0.81[ASN][1000 genomes]
rs380914	0.82[ASN][1000 genomes]
rs414205	0.81[ASN][1000 genomes]
rs4143771	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs420478	0.81[ASN][1000 genomes]
rs4289643	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs436827	0.81[ASN][1000 genomes]
rs450630	0.81[ASN][1000 genomes]
rs6456831	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6902736	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6925714	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6926221	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6926470	0.81[ASN][1000 genomes]
rs7381993	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7382112	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7382146	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7383248	0.92[EUR][1000 genomes]
rs7752875	0.87[EUR][1000 genomes]
rs9348810	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9368568	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9378185	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9380079	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9380083	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9393920	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9393921	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9501180	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9885928	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[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	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1031671	chr6:28575172-28678126	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1319075	ZKSCAN3	cis	parietal	SCAN
rs1319075	ZNF323	cis	parietal	SCAN
rs1319075	HIST1H2BL	cis	cerebellum	SCAN
rs1319075	ZSCAN23	cis	cerebellum	SCAN
rs1319075	ZNF192	cis	cerebellum	SCAN
rs1319075	ZKSCAN3	cis	cerebellum	SCAN
rs1319075	ZNF187	cis	cerebellum	SCAN
rs1319075	ZNF323	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28654200-28663600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:28658200-28667400	Weak transcription	K562	blood
3	chr6:28660800-28662800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr6:28661000-28662800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr6:28661000-28665000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr6:28661200-28662600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:28661200-28662600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
8	chr6:28661400-28662800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr6:28661600-28662600	Bivalent Enhancer	Fetal Muscle Leg	muscle
10	chr6:28661800-28662600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
11	chr6:28661800-28662600	Flanking Bivalent TSS/Enh	NHEK	skin
12	chr6:28662000-28662600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
13	chr6:28662000-28662800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
14	chr6:28662000-28663000	Bivalent Enhancer	Fetal Heart	heart
15	chr6:28662400-28662600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
16	chr6:28662400-28662600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
17	chr6:28662400-28662600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
18	chr6:28662400-28662600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:28662400-28662600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:28662400-28662600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:28662400-28662600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:28662400-28662800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
23	chr6:28662400-28662800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
24	chr6:28662400-28662800	Bivalent Enhancer	HepG2	liver
25	chr6:28662400-28663000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:28662400-28663000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:28662400-28663600	Weak transcription	Right Atrium	heart

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