Variant report

Variant	rs1967327
Chromosome Location	chr2:179314359-179314360
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:179314166-179316943	H1-hESC	embryonic stem cell:	n/a	n/a
2	SPI1	chr2:179314243-179315016	HL-60	blood:	n/a	chr2:179314478-179314491
3	POLR2A	chr2:179313314-179316831	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:179313913-179314495	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:179277180..179281325-chr2:179314213..179317479,5	K562	blood:
2	chr2:179310863..179318324-chr2:179338966..179346608,29	K562	blood:
3	chr2:178976419..178978821-chr2:179313368..179316809,4	K562	blood:
4	chr2:179313693..179317837-chr2:179319182..179322709,8	K562	blood:
5	chr2:179311363..179318324-chr2:179340414..179346232,28	K562	blood:
6	chr2:179278648..179281403-chr2:179313491..179316018,3	MCF-7	breast:
7	chr2:179312045..179317660-chr2:179337933..179347437,24	MCF-7	breast:
8	chr2:179276988..179281129-chr2:179311895..179317764,7	MCF-7	breast:
9	chr2:179314051..179317404-chr2:179386204..179389847,5	K562	blood:

No data

Variant related genes	Relation type
PRKRA	TF binding region
DFNB59	TF binding region
ENSG00000155636	Chromatin interaction
ENSG00000116095	Chromatin interaction
ENSG00000223960	Chromatin interaction
ENSG00000238082	Chromatin interaction
ENSG00000204311	Chromatin interaction
ENSG00000237298	Chromatin interaction
ENSG00000079150	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10188593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10930831	0.86[EUR][1000 genomes]
rs11688081	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs13382684	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13411588	0.91[GIH][hapmap];0.89[TSI][hapmap]
rs1559908	0.81[GIH][hapmap];0.85[TSI][hapmap]
rs16866334	0.81[GIH][hapmap];0.85[TSI][hapmap]
rs1863671	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2114581	0.82[YRI][hapmap]
rs2288320	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2303536	0.92[CEU][hapmap]
rs28773318	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2886712	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs33998881	0.82[AMR][1000 genomes]
rs3752689	0.95[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs3769867	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4894020	0.91[GIH][hapmap];0.89[TSI][hapmap]
rs57115861	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6704545	0.89[GIH][hapmap];0.85[TSI][hapmap]
rs6710856	0.81[EUR][1000 genomes]
rs6739142	0.95[GIH][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs6753709	0.95[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs6758838	0.80[EUR][1000 genomes]
rs7575643	1.00[CEU][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs7589565	0.91[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs7600176	0.91[GIH][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs8179648	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs9967820	0.92[CEU][hapmap];0.82[AMR][1000 genomes]
rs9973732	0.91[CHB][hapmap];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	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	esv1817469	chr2:179296271-179319391	Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	esv9296	chr2:179308042-179315047	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	esv3458780	chr2:179312167-179315082	Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	esv3458779	chr2:179312250-179314994	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
6	esv3445737	chr2:179312275-179314988	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
7	esv3458781	chr2:179312298-179314971	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	esv3458782	chr2:179312312-179314972	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1967327	CHAD	trans	brain	seeQTL
rs1967327	LIMA1	trans	brain	seeQTL
rs1967327	CACNA1A	trans	brain	seeQTL
rs1967327	FKBP7	cis	lymphoblastoid	seeQTL
rs1967327	PAX6	trans	brain	seeQTL
rs1967327	PCP2	trans	brain	seeQTL
rs1967327	CLCNKA	trans	brain	seeQTL
rs1967327	CBLN1	trans	brain	seeQTL
rs1967327	EOMES	trans	brain	seeQTL
rs1967327	DPF3	trans	brain	seeQTL
rs1967327	PLEKHA3	cis	lymphoblastoid	seeQTL
rs1967327	ATP2C2	trans	parietal	SCAN
rs1967327	ZNF385B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179280200-179314600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:179292000-179314600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:179298600-179314400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:179299600-179314800	Weak transcription	Small Intestine	intestine
5	chr2:179306200-179314400	Weak transcription	Psoas Muscle	Psoas
6	chr2:179310000-179314600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:179311000-179314800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:179311200-179314600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:179312600-179314400	Enhancers	Brain Germinal Matrix	brain
10	chr2:179312800-179314600	Enhancers	Fetal Heart	heart
11	chr2:179312800-179314600	Enhancers	Right Ventricle	heart
12	chr2:179313000-179314400	Enhancers	Brain Angular Gyrus	brain
13	chr2:179313000-179314400	Enhancers	Hela-S3	cervix
14	chr2:179313000-179314600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:179313000-179314600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:179313200-179314400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:179313200-179314400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:179313200-179314400	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr2:179313200-179314600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr2:179313400-179314400	Genic enhancers	Fetal Brain Male	brain
21	chr2:179313400-179314400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr2:179313400-179314400	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr2:179313400-179314600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:179313400-179314600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr2:179313400-179314600	Weak transcription	Esophagus	oesophagus
26	chr2:179313400-179314800	Weak transcription	Gastric	stomach
27	chr2:179313400-179315000	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:179313400-179315200	Transcr. at gene 5' and 3'	Dnd41	blood
29	chr2:179313600-179314400	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr2:179313600-179314400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:179313600-179314400	Enhancers	Duodenum Mucosa	Duodenum
32	chr2:179313600-179314400	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr2:179313600-179314600	Enhancers	Primary T cells fromperipheralblood	blood
34	chr2:179313600-179314600	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr2:179313600-179314600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:179313600-179314600	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr2:179313600-179314600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr2:179313600-179314600	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr2:179313600-179314600	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr2:179313600-179314600	Enhancers	Brain Substantia Nigra	brain
41	chr2:179313600-179314600	Enhancers	Fetal Kidney	kidney
42	chr2:179313600-179314600	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr2:179313600-179314600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:179313600-179315200	Flanking Active TSS	HMEC	breast
45	chr2:179313600-179316800	Active TSS	Aorta	Aorta
46	chr2:179313800-179314400	Enhancers	Primary hematopoietic stem cells	blood
47	chr2:179313800-179314400	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr2:179313800-179314400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:179313800-179314400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:179313800-179314400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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