Variant report

Variant	rs7978604
Chromosome Location	chr12:9001717-9001718
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10734734	0.84[EUR][1000 genomes]
rs10743504	0.84[EUR][1000 genomes]
rs11047510	0.84[EUR][1000 genomes]
rs11047578	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12296947	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17729632	0.84[EUR][1000 genomes]
rs17729753	0.88[CEU][hapmap]
rs17802399	0.84[EUR][1000 genomes]
rs1860927	0.85[EUR][1000 genomes]
rs1894814	0.83[EUR][1000 genomes]
rs4883181	0.80[MEX][hapmap]
rs4883186	0.81[EUR][1000 genomes]
rs4883187	0.84[EUR][1000 genomes]
rs55906630	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56230819	0.96[EUR][1000 genomes]
rs57785077	0.81[AMR][1000 genomes]
rs59908019	0.96[EUR][1000 genomes]
rs60175291	0.97[EUR][1000 genomes]
rs6487407	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7136690	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7300139	0.93[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7301996	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7302253	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7304994	0.90[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs7305259	0.85[EUR][1000 genomes]
rs7308811	0.88[CEU][hapmap];1.00[GIH][hapmap]
rs7311897	0.83[GIH][hapmap]
rs7957179	0.81[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7978604	M6PR	cis	parietal	SCAN
rs7978604	BCL2L14	cis	parietal	SCAN
rs7978604	ARPC1A	trans	parietal	SCAN
rs7978604	LOC171220	cis	parietal	SCAN
rs7978604	COPS7A	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:8982200-9022000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:8983400-9017600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:8987600-9004200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr12:8987600-9040000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr12:8987800-9002800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:8987800-9004800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr12:8987800-9012800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:8988200-9012800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:8994800-9016600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:8996000-9007000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:8996000-9040000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:8997600-9004200	Weak transcription	Brain Anterior Caudate	brain
13	chr12:8998000-9002200	Weak transcription	Adipose Nuclei	Adipose
14	chr12:8998000-9002200	Weak transcription	K562	blood
15	chr12:8998800-9014600	Weak transcription	Right Atrium	heart
16	chr12:8999000-9016400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:9000400-9003400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:9000800-9012400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr12:9001200-9010200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr12:9001200-9011600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:9001600-9004200	Weak transcription	Esophagus	oesophagus
22	chr12:9001600-9004800	Weak transcription	Brain Substantia Nigra	brain

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