Variant report

Variant	rs7251682
Chromosome Location	chr19:44716021-44716022
allele	A/G
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	SIX5	chr19:44716021-44717300	A549	lung:	n/a	chr19:44716594-44716603

No.	Distal block	Cell Line	Cell type
1	chr19:44256902..44259660-chr19:44715792..44718086,2	K562	blood:
2	chr19:44710790..44713844-chr19:44714955..44718823,7	MCF-7	breast:
3	chr19:44709921..44713618-chr19:44714834..44717350,4	K562	blood:

Variant related genes	Relation type
ZNF227	TF binding region
ENSG00000105771	Chromatin interaction
ENSG00000131115	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10405450	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10410086	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10423306	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10425945	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10775542	0.81[EUR][1000 genomes]
rs11666199	0.87[EUR][1000 genomes]
rs11667521	0.89[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs12459795	0.83[EUR][1000 genomes]
rs12460039	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12462557	0.89[CEU][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs12462723	0.89[CEU][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs12608984	0.81[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12972784	0.87[EUR][1000 genomes]
rs12975315	0.81[EUR][1000 genomes]
rs12975546	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs12980565	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs2051059	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs2085516	0.81[CHB][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs2100643	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2125578	0.82[EUR][1000 genomes]
rs2125579	0.89[CEU][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs2168989	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2232801	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2279072	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2279073	0.89[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs2293587	0.83[GIH][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.84[ASN][1000 genomes]
rs2356751	0.81[CHB][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.84[ASN][1000 genomes]
rs3817595	0.81[CHB][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.84[ASN][1000 genomes]
rs4802210	0.83[GIH][hapmap]
rs4802218	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs4803694	0.82[EUR][1000 genomes]
rs56357907	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs58778698	0.84[ASN][1000 genomes]
rs61412562	0.81[ASN][1000 genomes]
rs61589395	0.81[ASN][1000 genomes]
rs62117770	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6509146	0.81[CHB][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6509150	0.82[EUR][1000 genomes]
rs7248114	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7249209	0.81[CHB][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7253196	0.89[EUR][1000 genomes]
rs7253533	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7259916	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7260304	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8101032	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs8102037	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8105073	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs8106766	0.82[EUR][1000 genomes]
rs8108934	0.81[EUR][1000 genomes]
rs9304640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9646643	0.89[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7251682	SIX5	cis	cerebellum	SCAN
rs7251682	SAE1	cis	cerebellum	SCAN
rs7251682	SIGLEC16	cis	cerebellum	SCAN
rs7251682	C5AR1	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44712200-44716200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr19:44712200-44716200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr19:44712200-44716200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr19:44712200-44716200	Weak transcription	Brain Substantia Nigra	brain
5	chr19:44712200-44716600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr19:44712400-44716200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr19:44712400-44716200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr19:44712400-44716200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr19:44712400-44716200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr19:44712400-44716200	Weak transcription	Fetal Brain Female	brain
11	chr19:44712400-44716200	Weak transcription	HUVEC	blood vessel
12	chr19:44712600-44716200	Weak transcription	Brain Germinal Matrix	brain
13	chr19:44712600-44716200	Weak transcription	NHEK	skin
14	chr19:44712800-44716200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:44712800-44716200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr19:44712800-44716200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr19:44712800-44716200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr19:44712800-44716200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr19:44712800-44716200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr19:44712800-44716200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr19:44712800-44716200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr19:44712800-44716200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr19:44712800-44716200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr19:44712800-44716200	Weak transcription	Hela-S3	cervix
25	chr19:44712800-44716200	Weak transcription	Osteobl	bone
26	chr19:44712800-44716400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr19:44713000-44716200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr19:44713000-44716200	Weak transcription	Primary T cells from cord blood	blood
29	chr19:44713000-44716200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr19:44713000-44716200	Weak transcription	Fetal Lung	lung
31	chr19:44713000-44716200	Weak transcription	NHDF-Ad	bronchial
32	chr19:44713000-44716800	Weak transcription	Fetal Heart	heart
33	chr19:44713200-44716200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:44713200-44716200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr19:44713200-44716200	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr19:44713200-44716200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr19:44713200-44716200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr19:44713200-44716200	Weak transcription	K562	blood
39	chr19:44713400-44716200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:44715200-44717200	Active TSS	Liver	Liver
41	chr19:44715600-44716200	Enhancers	Dnd41	blood
42	chr19:44715600-44717400	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr19:44715600-44717400	Active TSS	A549	lung
44	chr19:44715800-44716400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr19:44715800-44717000	Active TSS	Adipose Nuclei	Adipose
46	chr19:44715800-44717400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr19:44715800-44717600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:44715800-44718200	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr19:44716000-44716200	Enhancers	Primary B cells from peripheral blood	blood
50	chr19:44716000-44716200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links