Variant report

Variant	rs2869872
Chromosome Location	chr4:77191112-77191113
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:77134728..77136600-chr4:77189748..77191379,2	K562	blood:
2	chr4:77184154..77186795-chr4:77189151..77191831,3	MCF-7	breast:
3	chr4:77185052..77186767-chr4:77189879..77191604,2	K562	blood:

Variant related genes	Relation type
ENSG00000138760	Chromatin interaction
ENSG00000272414	Chromatin interaction
ENSG00000189157	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1036787	0.90[AFR][1000 genomes]
rs1036788	1.00[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11097320	0.94[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1441911	0.84[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1441912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1441916	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1530295	0.86[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28592037	0.88[AFR][1000 genomes]
rs4370157	0.94[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4859440	0.84[ASN][1000 genomes]
rs4859658	0.94[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6532316	0.85[ASW][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs768981	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2869872	FAM47E	cis	parietal	SCAN
rs2869872	NAAA	cis	parietal	SCAN
rs2869872	FAM47E	cis	cerebellum	SCAN
rs2869872	SCARB2	cis	lymphoblastoid	seeQTL
rs2869872	CCNI	cis	lymphoblastoid	seeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77173600-77202000	Weak transcription	Psoas Muscle	Psoas
2	chr4:77173800-77191400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr4:77173800-77196000	Weak transcription	Adipose Nuclei	Adipose
4	chr4:77173800-77215800	Weak transcription	Brain Hippocampus Middle	brain
5	chr4:77177800-77199200	Weak transcription	Placenta	Placenta
6	chr4:77178800-77201200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:77180000-77202000	Weak transcription	Gastric	stomach
8	chr4:77182000-77194600	Weak transcription	Stomach Mucosa	stomach
9	chr4:77182400-77193400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr4:77183200-77193000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:77185000-77192600	Weak transcription	Left Ventricle	heart
12	chr4:77186400-77204200	Weak transcription	Aorta	Aorta
13	chr4:77186600-77196200	Weak transcription	Fetal Intestine Large	intestine
14	chr4:77186600-77196800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr4:77186600-77215000	Weak transcription	Brain Anterior Caudate	brain
16	chr4:77187000-77191600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:77187000-77196000	Weak transcription	Fetal Intestine Small	intestine
18	chr4:77187600-77202000	Weak transcription	Brain Substantia Nigra	brain
19	chr4:77187800-77193800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr4:77188000-77191800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:77188000-77202200	Weak transcription	Brain Angular Gyrus	brain
22	chr4:77188200-77202000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:77188400-77192000	Weak transcription	HepG2	liver
24	chr4:77188600-77193400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr4:77189000-77191400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr4:77190400-77199200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr4:77191000-77193000	Strong transcription	Skeletal Muscle Female	skeletal muscle

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