Variant report

Variant	rs11165030
Chromosome Location	chr1:94349077-94349078
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:94343685-94350802	A549	lung:	n/a	n/a
2	POLR2A	chr1:94343810-94352873	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:94336863..94338499-chr1:94348884..94351600,2	K562	blood:
2	chr1:94343582..94346281-chr1:94346551..94353410,8	MCF-7	breast:
3	chr1:94343831..94347542-chr1:94348227..94351449,4	MCF-7	breast:
4	chr1:94335805..94338499-chr1:94348129..94351600,3	K562	blood:

Variant related genes	Relation type
DNTTIP2	TF binding region
ENSG00000067334	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10874808	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10874809	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10874811	0.84[CHB][hapmap]
rs11165006	0.80[JPT][hapmap]
rs11165031	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs12083303	0.80[ASN][1000 genomes]
rs12122176	0.81[JPT][hapmap]
rs2064764	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2391323	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2391324	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs3170633	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.84[LWK][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3761912	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3827715	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs6667121	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675820	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6680315	0.82[ASN][1000 genomes]
rs6687387	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6689601	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6696758	0.84[CHB][hapmap]
rs718875	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7513671	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7515191	0.90[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7515813	0.84[ASN][1000 genomes]
rs7517826	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7533596	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7549683	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs769211	0.84[CHB][hapmap];0.82[JPT][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11165030	GEMIN8P4	cis	cerebellum	SCAN
rs11165030	GCLM	cis	parietal	SCAN
rs11165030	AI559539_RC	cis	multi-tissue	Pritchard

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94345000-94357000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:94345000-94374200	Weak transcription	Gastric	stomach
3	chr1:94345000-94374200	Weak transcription	Spleen	Spleen
4	chr1:94345200-94358800	Weak transcription	Left Ventricle	heart
5	chr1:94345200-94374000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:94345200-94374200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:94345400-94353600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:94345400-94353600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:94345400-94353600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr1:94345400-94354400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:94345400-94356600	Weak transcription	Aorta	Aorta
12	chr1:94345400-94356800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:94345400-94357000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:94345400-94357200	Weak transcription	NHLF	lung
15	chr1:94345400-94358800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:94345400-94359200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:94345400-94361000	Weak transcription	Fetal Thymus	thymus
18	chr1:94345400-94362000	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:94345400-94364000	Weak transcription	Fetal Intestine Small	intestine
20	chr1:94345400-94369400	Weak transcription	Colonic Mucosa	Colon
21	chr1:94345400-94373200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:94345400-94373200	Weak transcription	Brain Substantia Nigra	brain
23	chr1:94345400-94373800	Weak transcription	Fetal Stomach	stomach
24	chr1:94345400-94374000	Weak transcription	Right Ventricle	heart
25	chr1:94345600-94351200	Weak transcription	Liver	Liver
26	chr1:94345600-94353600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:94345600-94353600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:94345600-94353600	Weak transcription	HepG2	liver
29	chr1:94345600-94353600	Weak transcription	NHDF-Ad	bronchial
30	chr1:94345600-94353800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:94345600-94354000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:94345600-94354200	Weak transcription	Adipose Nuclei	Adipose
33	chr1:94345600-94354400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:94345600-94354400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:94345600-94354400	Weak transcription	K562	blood
36	chr1:94345600-94356200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:94345600-94356200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:94345600-94356200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:94345600-94356200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:94345600-94356200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr1:94345600-94356200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:94345600-94357600	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:94345600-94357800	Weak transcription	Hela-S3	cervix
44	chr1:94345600-94358400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr1:94345600-94358400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr1:94345600-94358600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:94345600-94358600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr1:94345600-94358600	Weak transcription	Fetal Intestine Large	intestine
49	chr1:94345600-94358600	Weak transcription	NHEK	skin
50	chr1:94345600-94358800	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links