Variant report

Variant	rs862996
Chromosome Location	chr1:159168609-159168610
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	chr1:159102004..159102751-chr1:159167774..159168846,3	MCF-7	breast:
2	chr1:159130507..159131704-chr1:159168609..159169447,4	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs3027012	0.88[CEU][hapmap]
rs6676002	0.88[CEU][hapmap]
rs862990	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs862991	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs862992	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs862994	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs862995	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs862999	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs862996	DARC	cis	cerebellum	SCAN
rs862996	PPOX	cis	cerebellum	SCAN
rs862996	PIGM	cis	cerebellum	SCAN
rs862996	KCNJ9	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	chr1:159159400-159169200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:159159600-159173200	Strong transcription	Fetal Brain Female	brain
8	chr1:159161800-159170000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:159163000-159173800	Weak transcription	Fetal Brain Male	brain
10	chr1:159163800-159169400	Weak transcription	Fetal Stomach	stomach
11	chr1:159164200-159172600	Strong transcription	Brain Germinal Matrix	brain
12	chr1:159167400-159168800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:159167600-159168800	Enhancers	Spleen	Spleen
14	chr1:159167600-159170000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:159167800-159169200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:159167800-159171200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:159168000-159174000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:159168000-159177600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:159168200-159169000	Strong transcription	Brain Anterior Caudate	brain
20	chr1:159168200-159170400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:159168200-159170400	Weak transcription	Thymus	Thymus
22	chr1:159168400-159168800	Genic enhancers	Brain Inferior Temporal Lobe	brain
23	chr1:159168400-159169400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:159168400-159169400	Weak transcription	Stomach Mucosa	stomach
25	chr1:159168400-159169600	Weak transcription	Fetal Thymus	thymus
26	chr1:159168400-159170200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:159168400-159171800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:159168400-159177600	Weak transcription	Brain Angular Gyrus	brain
29	chr1:159168600-159169600	Weak transcription	Placenta	Placenta
30	chr1:159168600-159169800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:159168600-159169800	Weak transcription	K562	blood
32	chr1:159168600-159170000	Weak transcription	Brain Hippocampus Middle	brain

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