Variant report

Variant	rs1978580
Chromosome Location	chr2:179348407-179348408
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:179347333..179349438-chr2:179354619..179356582,3	MCF-7	breast:
2	chr2:179343596..179347603-chr2:179348406..179354533,12	MCF-7	breast:
3	chr2:179315567..179317149-chr2:179346726..179348931,2	K562	blood:
4	chr2:179314116..179315931-chr2:179347973..179349774,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204311	Chromatin interaction
ENSG00000116095	Chromatin interaction
ENSG00000180228	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1001238	0.81[CHB][hapmap]
rs10207436	0.80[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs10930831	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12052983	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13411588	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs1559908	1.00[JPT][hapmap]
rs1560221	0.81[CHB][hapmap]
rs16866334	1.00[JPT][hapmap]
rs16866342	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16866400	0.81[CHB][hapmap]
rs16866420	0.81[CHB][hapmap]
rs2016615	0.98[ASN][1000 genomes]
rs2042996	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs2059691	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2114582	0.80[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap]
rs2163009	0.81[CHB][hapmap]
rs2249737	0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2288322	0.80[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.91[ASN][1000 genomes]
rs2303536	1.00[JPT][hapmap]
rs2303537	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2366751	0.81[CHB][hapmap]
rs2742351	0.82[CHB][hapmap]
rs2886712	0.85[ASN][1000 genomes]
rs33998881	0.81[ASN][1000 genomes]
rs3731750	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs3731754	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3752689	0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3769866	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3829746	0.81[CHB][hapmap]
rs4894017	0.90[JPT][hapmap]
rs4894020	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs4894029	0.81[CHB][hapmap]
rs4894030	0.82[CHB][hapmap]
rs58506841	0.82[ASN][1000 genomes]
rs60488846	0.81[ASN][1000 genomes]
rs6704545	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6710856	0.89[ASN][1000 genomes]
rs6723399	0.82[ASN][1000 genomes]
rs6726043	0.96[ASN][1000 genomes]
rs6739142	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs6753709	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6758838	0.88[ASN][1000 genomes]
rs7575643	1.00[JPT][hapmap]
rs7577862	1.00[JPT][hapmap]
rs7587593	0.96[ASN][1000 genomes]
rs7588593	0.81[ASN][1000 genomes]
rs7589679	1.00[JPT][hapmap]
rs7598228	1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7600176	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7602597	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs8179648	0.95[JPT][hapmap]
rs9288019	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs957875	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs967507	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9808377	0.81[CHB][hapmap]
rs9967820	1.00[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1978580	FKBP7	cis	lymphoblastoid	seeQTL
rs1978580	ATF2	cis	parietal	SCAN
rs1978580	PDE1A	cis	parietal	SCAN
rs1978580	PRKRA	cis	cerebellum	SCAN
rs1978580	PRKRA	Cis_1M	lymphoblastoid	RTeQTL
rs1978580	PRKRA	cis	lymphoblastoid	seeQTL
rs1978580	FKBP7	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179346000-179350200	Enhancers	Small Intestine	intestine
2	chr2:179346000-179355800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:179346200-179350000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:179346400-179349000	Enhancers	Primary T cells fromperipheralblood	blood
5	chr2:179346400-179349400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr2:179346400-179349400	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr2:179346400-179355800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:179346400-179358600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:179346400-179387800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:179346600-179349600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr2:179346600-179350200	Enhancers	Stomach Mucosa	stomach
12	chr2:179346600-179350400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr2:179346600-179351000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr2:179346600-179356200	Weak transcription	Colonic Mucosa	Colon
15	chr2:179346600-179358600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:179346800-179349400	Enhancers	Brain Anterior Caudate	brain
17	chr2:179346800-179349800	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr2:179346800-179349800	Enhancers	K562	blood
19	chr2:179346800-179350200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr2:179346800-179350200	Enhancers	Liver	Liver
21	chr2:179346800-179350200	Enhancers	Brain Substantia Nigra	brain
22	chr2:179346800-179350200	Enhancers	Right Ventricle	heart
23	chr2:179346800-179350400	Enhancers	Colon Smooth Muscle	Colon
24	chr2:179347000-179350800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:179347200-179349400	Weak transcription	NHLF	lung
26	chr2:179347200-179349600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:179347200-179349600	Enhancers	HepG2	liver
28	chr2:179347200-179349800	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr2:179347200-179349800	Enhancers	Left Ventricle	heart
30	chr2:179347200-179350200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:179347200-179350200	Enhancers	Right Atrium	heart
32	chr2:179347200-179350200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr2:179347200-179350200	Enhancers	A549	lung
34	chr2:179347200-179350400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:179347200-179354400	Weak transcription	Placenta	Placenta
36	chr2:179347200-179355800	Weak transcription	HMEC	breast
37	chr2:179347200-179356000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr2:179347200-179356000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:179347200-179358600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:179347200-179358600	Weak transcription	NHEK	skin
41	chr2:179347200-179358800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr2:179347400-179348600	Weak transcription	NHDF-Ad	bronchial
43	chr2:179347400-179348800	Enhancers	Stomach Smooth Muscle	stomach
44	chr2:179347400-179348800	Weak transcription	NH-A	brain
45	chr2:179347400-179349000	Weak transcription	Hela-S3	cervix
46	chr2:179347400-179349000	Weak transcription	HUVEC	blood vessel
47	chr2:179347400-179349200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr2:179347400-179349800	Enhancers	Ovary	ovary
49	chr2:179347400-179350200	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr2:179347400-179350400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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