Variant report

Variant	rs3900668
Chromosome Location	chr1:216859823-216859824
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10442689	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10746365	0.87[GIH][hapmap]
rs10779274	0.87[CEU][hapmap]
rs12042592	0.89[CHB][hapmap]
rs12728283	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1339341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1416612	0.89[ASW][hapmap];0.87[CEU][hapmap];0.83[CHB][hapmap];0.87[GIH][hapmap];0.81[LWK][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes]
rs1416613	0.87[CEU][hapmap];0.87[GIH][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap]
rs17043567	0.89[CHB][hapmap]
rs1953520	0.87[CEU][hapmap]
rs2211118	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];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2789725	0.90[ASW][hapmap];0.87[CEU][hapmap];0.96[GIH][hapmap];0.81[TSI][hapmap]
rs2813699	0.85[EUR][1000 genomes]
rs2813705	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2820883	0.87[CEU][hapmap];0.96[GIH][hapmap];0.81[TSI][hapmap]
rs2820884	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2820885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3929878	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4426040	0.87[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap]
rs4846631	0.87[CEU][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap]
rs946465	0.87[CEU][hapmap];0.80[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap]
rs946466	0.87[CEU][hapmap];0.80[TSI][hapmap]
rs946467	0.83[CHB][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3900668	ANGEL2	cis	parietal	SCAN
rs3900668	TGFB2	cis	parietal	SCAN
rs3900668	TGFB2	cis	cerebellum	SCAN

Chromatin state (count:21 , 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	chr1:216856400-216869800	Weak transcription	Psoas Muscle	Psoas
10	chr1:216856600-216860000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:216858800-216860200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr1:216858800-216860400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:216859000-216860000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:216859000-216860200	Enhancers	Fetal Heart	heart
15	chr1:216859000-216860400	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr1:216859200-216860000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr1:216859200-216860200	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr1:216859400-216860200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:216859800-216860200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:216859800-216861800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr1:216859800-216863600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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