Variant report

Variant	rs9396617
Chromosome Location	chr6:15924215-15924216
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15923596..15926466-chr6:15952289..15954964,2	K562	blood:
2	chr6:15922948..15926543-chr6:16128347..16132310,5	K562	blood:
3	chr6:15882525..15884862-chr6:15922870..15925036,2	K562	blood:
4	chr6:15915036..15924551-chr6:16129181..16135842,15	K562	blood:
5	chr6:15921762..15925061-chr6:15925136..15927911,3	MCF-7	breast:
6	chr6:15909137..15912614-chr6:15921343..15924377,3	K562	blood:

Variant related genes	Relation type
ENSG00000007944	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11966220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13208062	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[EUR][1000 genomes]
rs13214084	1.00[EUR][1000 genomes]
rs13220668	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2096212	1.00[ASN][1000 genomes]
rs28860300	1.00[EUR][1000 genomes]
rs34126499	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34301608	1.00[EUR][1000 genomes]
rs34545176	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35734382	1.00[EUR][1000 genomes]
rs4712266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[ASN][1000 genomes]
rs707840	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9349990	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358074	1.00[CEU][hapmap]
rs9370839	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs9370848	1.00[EUR][1000 genomes]
rs9383090	0.89[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs9383091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9383093	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[EUR][1000 genomes]
rs9383094	0.81[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9396616	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9396617	SH2D2A	trans	brain	seeQTL
rs9396617	SLC5A7	trans	brain	seeQTL
rs9396617	TTR	trans	brain	seeQTL
rs9396617	LRTM1	trans	brain	seeQTL
rs9396617	GUCA1C	trans	brain	seeQTL
rs9396617	CRX	trans	brain	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15920200-15924600	Enhancers	Placenta	Placenta
2	chr6:15921600-15924400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:15921600-15927600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:15921600-15929400	Weak transcription	Adipose Nuclei	Adipose
5	chr6:15922000-15924400	Enhancers	HUVEC	blood vessel
6	chr6:15922000-15926600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr6:15922200-15924400	Enhancers	K562	blood
8	chr6:15922600-15925200	Enhancers	Fetal Muscle Leg	muscle
9	chr6:15923600-15926600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:15923800-15925800	Weak transcription	Aorta	Aorta
11	chr6:15924000-15926400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:15924000-15926800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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