Variant report

Variant	rs9288174
Chromosome Location	chr2:191418198-191418199
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:191397324..191399612-chr2:191415383..191418342,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM194B-2	chr2:191417990-191418206	NONHSAT076090

Variant related genes	Relation type
ENSG00000189362	Chromatin interaction
ENSG00000233654	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10169169	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10171376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10173975	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179262	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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10185147	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10189140	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10202274	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10204342	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208737	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10209340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10211375	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737936	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap]
rs11553601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11695439	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[ASN][1000 genomes]
rs13031452	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13386210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13388162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13395233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13398741	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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13405215	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13410179	1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.94[ASN][1000 genomes]
rs13412663	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13412823	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13412835	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13412879	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13417310	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13418943	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13429315	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1837686	0.87[ASN][1000 genomes]
rs3811608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4283453	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4853712	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs56715527	0.84[ASN][1000 genomes]
rs58210597	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58253207	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58433478	0.92[ASN][1000 genomes]
rs58708643	0.87[ASN][1000 genomes]
rs6434401	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap]
rs6717050	0.97[ASN][1000 genomes]
rs72903349	0.82[ASN][1000 genomes]
rs72903383	0.86[ASN][1000 genomes]
rs72905242	0.92[ASN][1000 genomes]
rs73054092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560045	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562013	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7574844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584379	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594994	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7609330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs894072	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[ASN][1000 genomes]
rs8962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9967829	0.83[CEU][hapmap];0.82[CHB][hapmap]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9288174	TMEM194B	cis	cerebellum	SCAN
rs9288174	FLJ20160	Cis_1M	lymphoblastoid	RTeQTL
rs9288174	FLJ20160	cis	multi-tissue	Pritchard
rs9288174	MFSD6	cis	parietal	SCAN
rs9288174	MFSD6	cis	lymphoblastoid	seeQTL
rs9288174	ASNSD1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191410800-191418200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:191411000-191443000	Weak transcription	Right Atrium	heart
3	chr2:191416000-191418200	Enhancers	Primary T cells from cord blood	blood
4	chr2:191417000-191418800	Weak transcription	Gastric	stomach
5	chr2:191417000-191419000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:191417000-191419400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:191417600-191427800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:191418000-191418200	Enhancers	HepG2	liver
9	chr2:191418000-191427000	Weak transcription	Pancreas	Pancrea

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