Variant report

Variant	rs4767899
Chromosome Location	chr12:120905727-120905728
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:120905727-120905837	HepG2	liver:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120900995..120903574-chr12:120904583..120907524,5	MCF-7	breast:
2	chr12:120905582..120907293-chr12:121017585..121020465,2	K562	blood:
3	chr12:120874293..120878054-chr12:120905643..120908923,7	K562	blood:
4	chr12:120904864..120906819-chr12:120975505..120978250,2	K562	blood:
5	chr12:120727751..120732241-chr12:120903536..120914205,12	MCF-7	breast:
6	chr12:120727396..120732537-chr12:120902983..120911236,13	K562	blood:
7	chr12:120832590..120834451-chr12:120905005..120906685,2	MCF-7	breast:
8	chr12:120903651..120915747-chr12:120930491..120936868,24	K562	blood:
9	chr12:120873907..120875736-chr12:120904532..120906530,2	MCF-7	breast:
10	chr12:120726465..120732980-chr12:120904767..120910057,7	MCF-7	breast:
11	chr12:120728388..120731475-chr12:120905367..120907269,3	K562	blood:
12	chr12:120899786..120915162-chr12:120926090..120939394,54	MCF-7	breast:
13	chr12:120880802..120886804-chr12:120903895..120909908,12	K562	blood:
14	chr12:120903724..120908002-chr12:120939821..120944385,4	MCF-7	breast:
15	chr12:120905117..120912400-chr12:120930505..120935641,13	K562	blood:
16	chr12:120905660..120907924-chr12:120965439..120968401,2	MCF-7	breast:
17	chr12:120905412..120907184-chr12:120925601..120927838,2	K562	blood:
18	chr12:120905043..120908623-chr12:120970585..120973644,4	K562	blood:
19	chr12:120876128..120878173-chr12:120904219..120906337,2	K562	blood:

No data

Variant related genes	Relation type
SRSF9	TF binding region
DYNLL1	TF binding region
ENSG00000257218	Chromatin interaction
ENSG00000111775	Chromatin interaction
ENSG00000111780	Chromatin interaction
ENSG00000022840	Chromatin interaction
ENSG00000222601	Chromatin interaction
ENSG00000111786	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000167272	Chromatin interaction
ENSG00000170855	Chromatin interaction
ENSG00000110871	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000248008	Chromatin interaction
ENSG00000088986	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1037611	0.82[ASN][1000 genomes]
rs10774550	0.82[ASN][1000 genomes]
rs10774558	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11065147	0.82[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs11065157	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs11065158	0.95[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap]
rs1151845	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1167688	0.82[ASN][1000 genomes]
rs1167699	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs1167706	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs1167715	0.96[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs1179460	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs12369178	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap]
rs12423303	1.00[YRI][hapmap]
rs1592361	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1671762	0.82[ASN][1000 genomes]
rs16950058	1.00[YRI][hapmap]
rs16950065	1.00[YRI][hapmap]
rs1710142	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1710146	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1794752	0.82[ASN][1000 genomes]
rs2076022	0.89[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs2235223	0.81[ASN][1000 genomes]
rs2292680	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2301456	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2673625	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs28390349	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3088345	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs35801170	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3847971	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4767898	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs542407	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs606443	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs637799	0.89[JPT][hapmap]
rs667913	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs671566	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs680795	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7307666	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs787818	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs787821	0.82[ASN][1000 genomes]
rs787822	0.82[ASN][1000 genomes]
rs787823	0.82[ASN][1000 genomes]
rs787828	0.82[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs787830	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs7957424	0.80[CHB][hapmap]
rs9657936	1.00[YRI][hapmap]
rs9657941	1.00[YRI][hapmap]
rs9657942	1.00[YRI][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4767899	POP5	Cis_1M	lymphoblastoid	RTeQTL
rs4767899	RNF10	cis	multi-tissue	Pritchard
rs4767899	RNF10	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120885400-120906000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:120885400-120906000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:120888600-120905800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:120890400-120905800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:120891000-120905800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr12:120891200-120905800	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr12:120902000-120906000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:120902600-120905800	Weak transcription	Stomach Mucosa	stomach
9	chr12:120903400-120905800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:120903400-120905800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:120903400-120906000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:120903600-120905800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:120903600-120905800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
14	chr12:120903600-120905800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr12:120903600-120905800	Weak transcription	HSMMtube	muscle
16	chr12:120903600-120906000	Weak transcription	Brain Substantia Nigra	brain
17	chr12:120903600-120906000	Weak transcription	Esophagus	oesophagus
18	chr12:120903600-120906200	Weak transcription	Small Intestine	intestine
19	chr12:120903800-120905800	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr12:120903800-120906000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr12:120903800-120906000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:120903800-120906000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr12:120904000-120905800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:120904000-120905800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr12:120904000-120905800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:120904000-120905800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:120904000-120905800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:120904000-120905800	Enhancers	Brain Angular Gyrus	brain
29	chr12:120904000-120905800	Genic enhancers	Duodenum Mucosa	Duodenum
30	chr12:120904000-120905800	Genic enhancers	Fetal Stomach	stomach
31	chr12:120904000-120906000	Enhancers	Primary B cells from cord blood	blood
32	chr12:120904000-120906000	Enhancers	Colon Smooth Muscle	Colon
33	chr12:120904200-120905800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr12:120904200-120905800	Genic enhancers	Fetal Brain Female	brain
35	chr12:120904200-120906000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr12:120904200-120906000	Genic enhancers	Fetal Thymus	thymus
37	chr12:120904400-120905800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
38	chr12:120904400-120905800	Genic enhancers	Brain Anterior Caudate	brain
39	chr12:120904400-120905800	Genic enhancers	Hela-S3	cervix
40	chr12:120904400-120906000	Genic enhancers	Fetal Muscle Trunk	muscle
41	chr12:120904400-120906000	Genic enhancers	Rectal Mucosa Donor 29	rectum
42	chr12:120904600-120905800	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:120904600-120905800	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr12:120904600-120905800	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr12:120904600-120906000	Weak transcription	Fetal Lung	lung
46	chr12:120904600-120906600	Transcr. at gene 5' and 3'	Dnd41	blood
47	chr12:120904800-120905800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:120904800-120905800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
49	chr12:120904800-120905800	Genic enhancers	HUVEC	blood vessel
50	chr12:120904800-120905800	Genic enhancers	Osteobl	bone

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