Variant report

Variant	rs7260304
Chromosome Location	chr19:44717978-44717979
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44716557..44719060-chr19:45004270..45005814,2	MCF-7	breast:
2	chr19:44256902..44259660-chr19:44715792..44718086,2	K562	blood:
3	chr19:44710790..44713844-chr19:44714955..44718823,7	MCF-7	breast:
4	chr19:44717507..44719170-chr19:44774754..44776983,2	K562	blood:

Variant related genes	Relation type
ENSG00000167384	Chromatin interaction
ENSG00000105771	Chromatin interaction
ENSG00000131115	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10405450	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10410086	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10423306	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10425945	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11666199	0.85[EUR][1000 genomes]
rs11667521	0.89[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap]
rs12459795	0.85[EUR][1000 genomes]
rs12460039	0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12462557	0.88[CEU][hapmap];0.92[GIH][hapmap];0.86[TSI][hapmap]
rs12462723	0.89[CEU][hapmap];0.92[GIH][hapmap];0.86[TSI][hapmap]
rs12608984	0.81[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12972784	0.89[EUR][1000 genomes]
rs12975546	0.89[CEU][hapmap]
rs12980565	0.89[CEU][hapmap]
rs2051059	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs2085516	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2100643	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2125579	0.89[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap]
rs2168989	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2279072	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2279073	0.89[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap]
rs2293587	0.95[JPT][hapmap];0.80[YRI][hapmap];0.85[ASN][1000 genomes]
rs2356751	0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.85[ASN][1000 genomes]
rs3817595	0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.85[ASN][1000 genomes]
rs4802218	0.88[CEU][hapmap]
rs56357907	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs58778698	0.85[ASN][1000 genomes]
rs61412562	0.81[ASN][1000 genomes]
rs61589395	0.81[ASN][1000 genomes]
rs62117770	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6509146	0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7248114	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7249209	0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7251682	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]
rs7253196	0.86[EUR][1000 genomes]
rs7253533	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7259916	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8101032	0.89[CEU][hapmap]
rs8102037	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8105073	0.91[CEU][hapmap]
rs8108934	0.82[EUR][1000 genomes]
rs9304640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9646643	0.89[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7260304	SIX5	cis	cerebellum	SCAN
rs7260304	C5AR1	cis	parietal	SCAN
rs7260304	SAE1	cis	cerebellum	SCAN
rs7260304	SIGLEC16	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44715800-44718200	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr19:44716000-44718000	Active TSS	Psoas Muscle	Psoas
3	chr19:44716000-44718000	Active TSS	Right Ventricle	heart
4	chr19:44716000-44718200	Active TSS	Right Atrium	heart
5	chr19:44716200-44718000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr19:44716200-44718000	Active TSS	H1 Cell Line	embryonic stem cell
7	chr19:44716200-44718000	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr19:44716200-44718000	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr19:44716200-44718000	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr19:44716200-44718000	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr19:44716200-44718000	Active TSS	GM12878-XiMat	blood
12	chr19:44716200-44718000	Active TSS	K562	blood
13	chr19:44716200-44718000	Active TSS	NH-A	brain
14	chr19:44716200-44718000	Active TSS	NHLF	lung
15	chr19:44716200-44718200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr19:44716200-44718200	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr19:44716200-44718200	Active TSS	Brain Anterior Caudate	brain
18	chr19:44716200-44718200	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr19:44716200-44718200	Active TSS	NHDF-Ad	bronchial
20	chr19:44717000-44718000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr19:44717000-44718000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr19:44717000-44718200	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr19:44717000-44718200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr19:44717200-44718000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr19:44717200-44718000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr19:44717200-44718000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr19:44717200-44718000	Flanking Active TSS	Liver	Liver
28	chr19:44717200-44718000	Flanking Active TSS	Brain Angular Gyrus	brain
29	chr19:44717200-44718000	Flanking Active TSS	HUVEC	blood vessel
30	chr19:44717200-44718200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr19:44717200-44718200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr19:44717200-44718200	Flanking Active TSS	Thymus	Thymus
33	chr19:44717400-44718000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr19:44717400-44718000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr19:44717400-44718000	Flanking Active TSS	Fetal Brain Female	brain
36	chr19:44717400-44718000	Flanking Active TSS	A549	lung
37	chr19:44717400-44718200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr19:44717400-44718200	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr19:44717400-44718200	Enhancers	Placenta Amnion	Placenta Amnion
40	chr19:44717400-44718200	Transcr. at gene 5' and 3'	Dnd41	blood
41	chr19:44717400-44718600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr19:44717400-44718600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr19:44717400-44718800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:44717400-44718800	Weak transcription	Esophagus	oesophagus
45	chr19:44717400-44718800	Weak transcription	Lung	lung
46	chr19:44717400-44719000	Weak transcription	Gastric	stomach
47	chr19:44717400-44719000	Weak transcription	Spleen	Spleen
48	chr19:44717400-44739000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr19:44717600-44718000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:44717600-44718000	Flanking Active TSS	Brain Cingulate Gyrus	brain

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