Variant report

Variant	rs3027001
Chromosome Location	chr1:159169463-159169464
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:159162126..159163793-chr1:159168944..159171497,2	K562	blood:

Extended variants
information (count: 7 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2249866	0.86[CEU][hapmap]
rs2249872	0.86[CEU][hapmap]
rs2253114	0.82[CEU][hapmap]
rs2253837	0.80[EUR][1000 genomes]
rs2852714	0.82[CEU][hapmap]
rs3026996	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656165	0.81[CEU][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3027001	LENEP	cis	parietal	SCAN
rs3027001	SLAMF7	cis	parietal	SCAN
rs3027001	ZFP28	trans	parietal	SCAN
rs3027001	SYT11	cis	parietal	SCAN
rs3027001	CCT3	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159158400-159174000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:159158800-159171200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:159158800-159177600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:159158800-159177800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:159158800-159188800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:159159600-159173200	Strong transcription	Fetal Brain Female	brain
7	chr1:159161800-159170000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr1:159163000-159173800	Weak transcription	Fetal Brain Male	brain
9	chr1:159164200-159172600	Strong transcription	Brain Germinal Matrix	brain
10	chr1:159167600-159170000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:159167800-159171200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:159168000-159174000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:159168000-159177600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:159168200-159170400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:159168200-159170400	Weak transcription	Thymus	Thymus
16	chr1:159168400-159169600	Weak transcription	Fetal Thymus	thymus
17	chr1:159168400-159170200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:159168400-159171800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:159168400-159177600	Weak transcription	Brain Angular Gyrus	brain
20	chr1:159168600-159169600	Weak transcription	Placenta	Placenta
21	chr1:159168600-159169800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:159168600-159169800	Weak transcription	K562	blood
23	chr1:159168600-159170000	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:159168800-159169600	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr1:159168800-159170600	Weak transcription	Spleen	Spleen
26	chr1:159169000-159170200	Weak transcription	Brain Anterior Caudate	brain
27	chr1:159169200-159170200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:159169200-159170400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:159169200-159170800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:159169400-159170000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:159169400-159170000	Enhancers	Stomach Mucosa	stomach
32	chr1:159169400-159170400	Strong transcription	Fetal Stomach	stomach

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