Variant report

Variant	rs6676002
Chromosome Location	chr1:159173144-159173145
allele	C/T
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]
rs10489849	0.91[ASN][1000 genomes]
rs11265150	0.91[ASN][1000 genomes]
rs12063098	0.83[ASN][1000 genomes]
rs12095174	0.91[ASN][1000 genomes]
rs12410844	0.83[ASN][1000 genomes]
rs2814778	1.00[LWK][hapmap]
rs3027008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3027012	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3027034	1.00[ASN][1000 genomes]
rs3027076	0.91[ASN][1000 genomes]
rs34029634	0.83[ASN][1000 genomes]
rs34217855	0.83[ASN][1000 genomes]
rs34683667	0.91[ASN][1000 genomes]
rs35113846	0.91[ASN][1000 genomes]
rs35333710	1.00[ASN][1000 genomes]
rs35405068	0.91[ASN][1000 genomes]
rs35610895	0.91[ASN][1000 genomes]
rs6687584	0.91[ASN][1000 genomes]
rs6687589	0.91[ASN][1000 genomes]
rs7533790	0.83[ASN][1000 genomes]
rs862990	0.88[CEU][hapmap]
rs862991	0.83[CEU][hapmap]
rs862996	0.88[CEU][hapmap]
rs862999	0.88[CEU][hapmap]
rs863002	1.00[LWK][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6676002	KCNJ9	cis	parietal	SCAN
rs6676002	PIGM	cis	cerebellum	SCAN

Chromatin state (count:29 , 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	chr1:159158800-159177600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:159158800-159177800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:159158800-159188800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:159159600-159173200	Strong transcription	Fetal Brain Female	brain
6	chr1:159163000-159173800	Weak transcription	Fetal Brain Male	brain
7	chr1:159168000-159174000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:159168000-159177600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:159168400-159177600	Weak transcription	Brain Angular Gyrus	brain
10	chr1:159170400-159173400	Weak transcription	Fetal Stomach	stomach
11	chr1:159170400-159173600	Weak transcription	Brain Anterior Caudate	brain
12	chr1:159170400-159174200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:159170400-159177800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:159170800-159174400	Enhancers	Lung	lung
15	chr1:159170800-159177600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:159171000-159173400	Bivalent Enhancer	Placenta	Placenta
17	chr1:159171400-159174800	Weak transcription	Esophagus	oesophagus
18	chr1:159171800-159174800	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr1:159171800-159176000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:159172000-159173200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:159172200-159174400	Enhancers	Spleen	Spleen
22	chr1:159172200-159175800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:159172400-159173600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr1:159172400-159174000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr1:159172600-159173400	Enhancers	K562	blood
26	chr1:159172600-159173600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:159172600-159177200	Weak transcription	Brain Germinal Matrix	brain
28	chr1:159173000-159173200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
29	chr1:159173000-159176400	Enhancers	GM12878-XiMat	blood

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