Variant report

Variant	rs4767884
Chromosome Location	chr12:120661977-120661978
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:120661126-120671187	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr12:120661634-120662592	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr12:120661800-120663088	Hela-S3	cervix:	n/a	n/a
4	ZNF263	chr12:120661264-120662633	HEK293-T-REx	kidney:	n/a	n/a
5	POLR2A	chr12:120661913-120663084	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr12:120661113-120662097	U87	brain:	n/a	n/a
7	POLR2A	chr12:120661780-120663894	K562	blood:	n/a	n/a
8	POLR2A	chr12:120661440-120664328	Hela-S3	cervix:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120642171..120684465-chr12:120719749..120734210,267	K562	blood:
2	chr12:120628211..120641965-chr12:120660551..120674110,39	K562	blood:
3	chr12:120656223..120689871-chr12:120720394..120738112,311	MCF-7	breast:
4	chr12:120657004..120683911-chr12:120723753..120737731,232	K562	blood:

No data

Variant related genes	Relation type
PXN	TF binding region
ENSG00000202538	Chromatin interaction
ENSG00000255857	Chromatin interaction
ENSG00000089154	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000123009	Chromatin interaction
ENSG00000089157	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10735071	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs10774543	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12308065	0.92[ASN][1000 genomes]
rs2286046	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];1.00[ASN][1000 genomes]
rs2696029	1.00[JPT][hapmap]
rs3845191	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847968	1.00[YRI][hapmap]
rs3956837	1.00[ASN][1000 genomes]
rs4766959	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6490286	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490287	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7298516	1.00[JPT][hapmap]
rs7960843	0.92[ASN][1000 genomes]
rs7968689	0.92[ASN][1000 genomes]
rs7978656	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs965791	1.00[JPT][hapmap]

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	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
4	nsv519657	chr12:120533696-120676090	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv560433	chr12:120533696-120676090	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	nsv832530	chr12:120586069-120758175	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	484 gene(s)	inside rSNPs	diseases
7	nsv1035698	chr12:120645330-120777580	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases
8	nsv1047447	chr12:120645330-120808621	Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4767884	ZNF828	trans	parietal	SCAN
rs4767884	GCN1L1	cis	parietal	SCAN
rs4767884	CABP1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120640200-120662400	Weak transcription	Fetal Brain Male	brain
2	chr12:120644000-120662600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:120646400-120662400	Weak transcription	Right Atrium	heart
4	chr12:120647600-120662000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:120647600-120662000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr12:120647600-120662000	Strong transcription	Adipose Nuclei	Adipose
7	chr12:120647600-120662600	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr12:120647600-120662600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr12:120647600-120662600	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr12:120647600-120662600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:120647800-120662200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr12:120648000-120662200	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr12:120648000-120662800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr12:120648000-120662800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr12:120648200-120662200	Strong transcription	Fetal Stomach	stomach
16	chr12:120655200-120662600	Strong transcription	NHDF-Ad	bronchial
17	chr12:120655200-120665400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr12:120655800-120662400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
19	chr12:120656200-120662600	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr12:120656200-120663200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:120656400-120662000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:120656400-120662000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:120656400-120662000	Strong transcription	Colon Smooth Muscle	Colon
24	chr12:120656400-120662000	Strong transcription	Ovary	ovary
25	chr12:120656400-120662200	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr12:120656400-120662400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:120656400-120662400	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr12:120656400-120664800	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr12:120656600-120662000	Strong transcription	A549	lung
30	chr12:120656600-120662200	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr12:120656600-120662400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
32	chr12:120656600-120663000	Strong transcription	NHLF	lung
33	chr12:120656800-120662000	Strong transcription	Thymus	Thymus
34	chr12:120656800-120662800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
35	chr12:120656800-120666000	Weak transcription	Fetal Kidney	kidney
36	chr12:120657000-120662200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:120657200-120662600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:120658000-120662400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
39	chr12:120659200-120662000	Strong transcription	Psoas Muscle	Psoas
40	chr12:120659400-120662000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:120659400-120662000	Strong transcription	Brain Angular Gyrus	brain
42	chr12:120659400-120663000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr12:120659600-120662000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:120659600-120662200	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr12:120659600-120662200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:120660000-120662000	Weak transcription	Primary B cells from cord blood	blood
47	chr12:120660000-120662000	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr12:120660400-120662600	Weak transcription	Brain Germinal Matrix	brain
49	chr12:120660400-120666000	Weak transcription	Dnd41	blood
50	chr12:120660600-120662200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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