Variant report

Variant	rs9288935
Chromosome Location	chr3:111772292-111772293
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10934131	0.80[CEU][hapmap];0.93[JPT][hapmap]
rs10934132	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10934133	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11711986	0.90[ASN][1000 genomes]
rs11711987	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11713084	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11713897	0.80[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11716665	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720631	0.80[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11927988	0.90[CEU][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes]
rs11928025	1.00[CEU][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12489437	0.90[CEU][hapmap];0.93[JPT][hapmap]
rs16859113	0.93[ASN][1000 genomes]
rs16859114	0.93[ASN][1000 genomes]
rs16859115	0.80[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16859117	0.93[ASN][1000 genomes]
rs16859126	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17443294	0.93[ASN][1000 genomes]
rs17443498	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17502804	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs4682081	0.85[CEU][hapmap]
rs4682351	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4682352	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4682353	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs73853294	0.93[ASN][1000 genomes]
rs7622025	0.90[CEU][hapmap];0.93[JPT][hapmap]
rs7630245	0.90[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap]
rs920708	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9829091	0.83[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9288935	CD200	cis	parietal	SCAN
rs9288935	GCET2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111763200-111772800	Weak transcription	Thymus	Thymus
2	chr3:111768000-111779800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:111768600-111772800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:111770600-111772600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:111770800-111772800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:111771000-111772600	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr3:111771000-111772800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:111771200-111772400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:111771200-111772400	Enhancers	Fetal Intestine Small	intestine
10	chr3:111771200-111772400	Enhancers	Fetal Thymus	thymus
11	chr3:111771200-111772600	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr3:111771200-111773200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr3:111771400-111772400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr3:111771400-111772600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr3:111771600-111773000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:111772000-111774000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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