Variant report

Variant	rs10207436
Chromosome Location	chr2:179294611-179294612
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:179292206..179295495-chr2:179302898..179306036,3	K562	blood:
2	chr2:179290672..179296705-chr2:179311873..179319969,11	K562	blood:
3	chr2:179290293..179297501-chr2:179307356..179318778,14	K562	blood:
4	chr2:179291608..179296531-chr2:179313533..179317372,6	MCF-7	breast:
5	chr2:179293578..179297906-chr2:179298629..179301854,4	K562	blood:
6	chr2:179289040..179292034-chr2:179292711..179296035,3	MCF-7	breast:
7	chr2:179293591..179296223-chr2:179303267..179306036,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000204311	Chromatin interaction
ENSG00000180228	Chromatin interaction
ENSG00000238082	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10179153	0.97[ASN][1000 genomes]
rs10930831	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs12052983	0.80[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs13411588	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[ASN][1000 genomes]
rs1559908	1.00[JPT][hapmap]
rs16866334	1.00[JPT][hapmap]
rs16866342	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1978580	0.80[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs2042996	0.84[JPT][hapmap]
rs2059691	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2114582	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2249737	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2288322	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2303536	1.00[JPT][hapmap]
rs2303537	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap]
rs2366603	0.96[ASN][1000 genomes]
rs2366604	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2886712	0.84[ASN][1000 genomes]
rs3731750	0.84[JPT][hapmap]
rs3731754	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs3752689	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[YRI][hapmap];0.84[ASN][1000 genomes]
rs3769866	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs4894017	0.86[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs4894018	0.96[ASN][1000 genomes]
rs4894019	0.96[ASN][1000 genomes]
rs4894020	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[ASN][1000 genomes]
rs6704545	0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6710856	0.80[ASN][1000 genomes]
rs6720559	0.83[YRI][hapmap]
rs6739142	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]
rs6753709	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs7575643	1.00[JPT][hapmap]
rs7577862	1.00[JPT][hapmap]
rs7589679	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[ASN][1000 genomes]
rs7598228	1.00[JPT][hapmap]
rs7600176	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[ASN][1000 genomes]
rs8179648	0.95[JPT][hapmap]
rs9288019	0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs957875	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs967507	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9967820	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv979349	chr2:179279539-179296355	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10207436	PRKRA	cis	lymphoblastoid	seeQTL
rs10207436	FKBP7	cis	lymphoblastoid	seeQTL
rs10207436	SSFA2	cis	cerebellum	SCAN
rs10207436	PRKRA	Cis_1M	lymphoblastoid	RTeQTL
rs10207436	ATP2C2	trans	parietal	SCAN
rs10207436	FKBP7	cis	parietal	SCAN
rs10207436	PRKRA	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179278800-179298800	Weak transcription	Small Intestine	intestine
2	chr2:179279600-179295000	Weak transcription	Right Ventricle	heart
3	chr2:179279600-179298800	Weak transcription	Colonic Mucosa	Colon
4	chr2:179279800-179295400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:179279800-179299200	Weak transcription	Esophagus	oesophagus
6	chr2:179279800-179313800	Weak transcription	Stomach Mucosa	stomach
7	chr2:179280000-179296800	Weak transcription	NHLF	lung
8	chr2:179280000-179297600	Weak transcription	Hela-S3	cervix
9	chr2:179280000-179298400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:179280000-179305200	Weak transcription	Fetal Brain Male	brain
11	chr2:179280000-179310600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:179280200-179296600	Weak transcription	Fetal Kidney	kidney
13	chr2:179280200-179314600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:179284400-179295400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:179287600-179295200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:179290200-179312800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:179290400-179294800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:179290400-179296600	Weak transcription	Psoas Muscle	Psoas
19	chr2:179290600-179296400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:179290800-179312000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr2:179290800-179312600	Strong transcription	Dnd41	blood
22	chr2:179291000-179300600	Strong transcription	Thymus	Thymus
23	chr2:179291000-179300800	Strong transcription	Stomach Smooth Muscle	stomach
24	chr2:179291000-179311600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:179291000-179313200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr2:179291000-179313400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:179291000-179313600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr2:179291200-179296400	Strong transcription	Fetal Stomach	stomach
29	chr2:179291200-179298400	Weak transcription	Fetal Intestine Small	intestine
30	chr2:179291200-179299600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:179291200-179300600	Strong transcription	Fetal Muscle Trunk	muscle
32	chr2:179291200-179300600	Strong transcription	Fetal Muscle Leg	muscle
33	chr2:179291200-179300600	Strong transcription	Left Ventricle	heart
34	chr2:179291200-179301200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:179291200-179303200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr2:179291200-179303200	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:179291200-179303800	Strong transcription	Primary T cells from cord blood	blood
38	chr2:179291200-179306200	Strong transcription	Fetal Brain Female	brain
39	chr2:179291200-179310400	Strong transcription	Primary B cells from peripheral blood	blood
40	chr2:179291200-179312200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr2:179291200-179312800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:179291200-179312800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:179291200-179312800	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr2:179291200-179313600	Strong transcription	Fetal Thymus	thymus
45	chr2:179291200-179313800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:179291400-179296000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:179291400-179296200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr2:179291400-179300800	Strong transcription	Brain Germinal Matrix	brain
49	chr2:179291400-179303000	Strong transcription	A549	lung
50	chr2:179291400-179311400	Strong transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links