Variant report

Variant	rs17043466
Chromosome Location	chr1:216878845-216878846
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10863269	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs11117646	0.88[CHB][hapmap]
rs11117649	0.88[CHB][hapmap]
rs11117669	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs11572715	0.82[YRI][hapmap]
rs12060770	0.87[CEU][hapmap];0.88[CHB][hapmap]
rs12070175	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs17043393	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17043436	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17043570	0.86[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap]
rs2066108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2789721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2789722	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2813666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2813670	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2813711	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2820881	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2820882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2999503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61817046	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61817047	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7538424	0.88[CHB][hapmap]
rs7543361	0.88[CHB][hapmap]
rs7550534	0.88[CHB][hapmap]
rs946468	0.88[CHB][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17043466	TGFB2	cis	cerebellum	SCAN
rs17043466	SMYD2	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216868200-216894000	Weak transcription	Placenta	Placenta
2	chr1:216874400-216879400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:216874800-216879000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:216875000-216879000	Weak transcription	Gastric	stomach
5	chr1:216875200-216879000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:216875200-216879200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:216875200-216879200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:216875200-216879200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:216875400-216879000	Weak transcription	Fetal Heart	heart
10	chr1:216878800-216879000	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr1:216878800-216879400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr1:216878800-216879600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:216878800-216879600	Enhancers	Fetal Brain Male	brain
14	chr1:216878800-216879600	Enhancers	NHEK	skin
15	chr1:216878800-216879800	Enhancers	Fetal Brain Female	brain
16	chr1:216878800-216880000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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