Variant report

Variant	rs17043350
Chromosome Location	chr1:216859096-216859097
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	chr1:216852250..216854082-chr1:216857827..216859800,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11117642	0.89[GIH][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.81[AMR][1000 genomes]
rs11117643	0.81[CHB][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes]
rs11117656	0.89[YRI][hapmap];0.87[AMR][1000 genomes]
rs12027901	0.81[CHB][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap]
rs12028510	0.80[CHB][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap];0.85[AMR][1000 genomes]
rs12754372	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1498278	0.93[YRI][hapmap];0.80[AMR][1000 genomes]
rs2789718	0.81[CHB][hapmap];0.89[GIH][hapmap]
rs2820879	0.81[CHB][hapmap];0.89[GIH][hapmap]
rs4846616	0.89[GIH][hapmap]
rs4846617	0.80[CHB][hapmap]
rs4846644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17043350	USH2A	cis	cerebellum	SCAN
rs17043350	TMEM194B	trans	lymphoblastoid	seeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216834400-216860400	Weak transcription	Right Ventricle	heart
2	chr1:216840200-216863600	Weak transcription	Fetal Intestine Small	intestine
3	chr1:216844000-216860000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:216844200-216861000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:216850800-216860000	Weak transcription	Left Ventricle	heart
6	chr1:216851000-216866000	Weak transcription	Placenta	Placenta
7	chr1:216854000-216860000	Weak transcription	Pancreas	Pancrea
8	chr1:216855600-216860800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:216856200-216859200	Enhancers	Pancreatic Islets	Pancreatic Islet
10	chr1:216856400-216859200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:216856400-216859200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:216856400-216869800	Weak transcription	Psoas Muscle	Psoas
13	chr1:216856600-216860000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:216858800-216859400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:216858800-216860200	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr1:216858800-216860400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:216859000-216859800	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr1:216859000-216860000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:216859000-216860200	Enhancers	Fetal Heart	heart
20	chr1:216859000-216860400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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