Variant report

Variant	rs1054607
Chromosome Location	chr6:109814411-109814412
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:109803960..109806635-chr6:109814001..109815992,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112365	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10080533	0.81[AFR][1000 genomes]
rs10457192	0.85[JPT][hapmap]
rs1046943	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.91[MKK][hapmap];0.90[YRI][hapmap];0.92[ASN][1000 genomes]
rs11251	0.82[JPT][hapmap]
rs11754455	0.80[JPT][hapmap]
rs1303981	0.81[AFR][1000 genomes]
rs13201430	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1322815	0.87[GIH][hapmap]
rs1406955	0.82[CEU][hapmap]
rs1476387	0.82[JPT][hapmap];0.81[MKK][hapmap];0.85[YRI][hapmap]
rs17070591	0.90[YRI][hapmap]
rs17070656	0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs2076929	0.94[YRI][hapmap]
rs2236084	0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.91[MKK][hapmap];0.90[YRI][hapmap];0.92[ASN][1000 genomes]
rs2277113	0.82[JPT][hapmap];0.90[YRI][hapmap]
rs35146243	0.92[ASN][1000 genomes]
rs3734652	0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.91[MKK][hapmap];0.90[YRI][hapmap];0.92[ASN][1000 genomes]
rs3757235	0.85[YRI][hapmap]
rs3778474	0.82[JPT][hapmap]
rs3778478	0.92[ASN][1000 genomes]
rs3799842	0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.91[MKK][hapmap];0.85[YRI][hapmap];0.92[ASN][1000 genomes]
rs60640103	0.85[AFR][1000 genomes]
rs6568587	0.95[YRI][hapmap]
rs6906216	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6911838	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs6917383	0.95[YRI][hapmap]
rs6917713	0.81[AFR][1000 genomes]
rs6920372	0.85[YRI][hapmap]
rs6920712	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925005	0.92[ASW][hapmap];0.95[YRI][hapmap]
rs6926096	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6939548	0.92[ASN][1000 genomes]
rs730089	0.85[YRI][hapmap]
rs7356790	0.92[ASW][hapmap];0.95[YRI][hapmap]
rs736830	0.85[YRI][hapmap]
rs7748669	0.82[JPT][hapmap]
rs7754650	0.82[JPT][hapmap]
rs7757895	0.87[GIH][hapmap];0.83[TSI][hapmap]
rs7765916	0.95[YRI][hapmap]
rs7767805	0.85[ASW][hapmap]
rs7768577	0.81[AFR][1000 genomes]
rs910730	0.81[MKK][hapmap];0.85[YRI][hapmap]
rs9320289	0.85[AFR][1000 genomes]
rs9320292	0.85[AFR][1000 genomes]
rs9372223	0.87[GIH][hapmap];0.83[TSI][hapmap]
rs9374111	0.87[GIH][hapmap];0.83[TSI][hapmap]
rs9384712	0.83[CEU][hapmap]
rs9384719	0.87[GIH][hapmap];0.83[TSI][hapmap]
rs9386810	0.81[AFR][1000 genomes]
rs9386822	0.87[GIH][hapmap];0.83[TSI][hapmap]
rs9386828	0.87[GIH][hapmap];0.83[TSI][hapmap]
rs9386829	0.87[GIH][hapmap];0.83[TSI][hapmap]
rs9398210	0.87[GIH][hapmap];0.83[TSI][hapmap]
rs9400284	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9400285	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9400287	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9480947	0.85[YRI][hapmap]
rs9480956	0.94[YRI][hapmap]
rs9480969	0.81[AFR][1000 genomes]
rs9487103	0.86[YRI][hapmap]
rs9791241	0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.91[MKK][hapmap];0.90[YRI][hapmap];0.92[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1054607	FLJ25791	cis	multi-tissue	Pritchard
rs1054607	GTF3C6	cis	cerebellum	SCAN
rs1054607	RFPL4B	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109805000-109817000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:109811600-109815000	Weak transcription	Primary B cells from peripheral blood	blood
3	chr6:109812000-109816800	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr6:109812600-109814600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:109812800-109816800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr6:109812800-109819000	Weak transcription	Fetal Kidney	kidney
7	chr6:109813000-109814600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:109813200-109816000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr6:109813400-109814800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:109813400-109815000	Weak transcription	Primary B cells from cord blood	blood
11	chr6:109813400-109815200	Weak transcription	K562	blood
12	chr6:109813400-109815400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:109813400-109816800	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:109813400-109817000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:109813400-109817000	Weak transcription	Primary T cells from cord blood	blood
16	chr6:109813400-109817400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:109813400-109817400	Weak transcription	Placenta	Placenta
18	chr6:109813400-109817400	Weak transcription	HSMMtube	muscle
19	chr6:109813400-109818000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:109813400-109821200	Weak transcription	Thymus	Thymus
21	chr6:109813400-109823000	Weak transcription	HSMM	muscle
22	chr6:109813600-109814600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr6:109813600-109814600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr6:109813600-109814600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:109813600-109814600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:109813600-109815200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr6:109813600-109815200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:109813600-109817400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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