Variant report

Variant	rs6849069
Chromosome Location	chr4:77179518-77179519
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:77156486..77158714-chr4:77178616..77181802,3	MCF-7	breast:
2	chr4:77171208..77175531-chr4:77176138..77180024,6	K562	blood:
3	chr4:77171623..77174207-chr4:77177725..77179646,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272414	Chromatin interaction
ENSG00000189157	Chromatin interaction
ENSG00000118804	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11097313	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs11097314	0.82[ASN][1000 genomes]
rs12643261	0.83[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs12651582	0.83[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs13122345	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs13137733	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1441910	0.81[JPT][hapmap]
rs1441914	0.81[JPT][hapmap]
rs17235935	0.84[CEU][hapmap]
rs17236158	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs17308336	0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1876536	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1876537	0.82[ASN][1000 genomes]
rs1876539	0.81[JPT][hapmap]
rs2119731	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119732	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289514	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2869863	0.83[ASN][1000 genomes]
rs2869864	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2869865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2904221	0.80[YRI][hapmap]
rs34034456	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34638846	0.83[ASN][1000 genomes]
rs3733250	0.81[JPT][hapmap]
rs4859643	0.92[CEU][hapmap]
rs4859650	0.82[ASN][1000 genomes]
rs4859651	0.82[ASN][1000 genomes]
rs4859652	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4859653	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56060342	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58804635	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60397621	0.82[ASN][1000 genomes]
rs6813980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814195	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823078	0.81[JPT][hapmap]
rs6835986	0.84[CEU][hapmap]
rs6851219	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs71607346	0.83[ASN][1000 genomes]
rs717239	0.80[CEU][hapmap]
rs7655112	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7677256	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7687964	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2760851	chr4:77164549-77185144	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6849069	SHROOM3	cis	parietal	SCAN
rs6849069	FAM47E	cis	cerebellum	SCAN
rs6849069	FAM47E	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77173600-77202000	Weak transcription	Psoas Muscle	Psoas
2	chr4:77173800-77185200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr4:77173800-77185400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr4:77173800-77185400	Weak transcription	Brain Anterior Caudate	brain
5	chr4:77173800-77186000	Weak transcription	Pancreas	Pancrea
6	chr4:77173800-77191400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:77173800-77196000	Weak transcription	Adipose Nuclei	Adipose
8	chr4:77173800-77215800	Weak transcription	Brain Hippocampus Middle	brain
9	chr4:77174000-77185600	Weak transcription	Brain Angular Gyrus	brain
10	chr4:77174200-77186000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:77176200-77186400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr4:77177800-77179600	Enhancers	HepG2	liver
13	chr4:77177800-77185400	Weak transcription	Aorta	Aorta
14	chr4:77177800-77199200	Weak transcription	Placenta	Placenta
15	chr4:77178400-77181600	Weak transcription	Stomach Mucosa	stomach
16	chr4:77178800-77179800	Weak transcription	Fetal Intestine Small	intestine
17	chr4:77178800-77185200	Weak transcription	Fetal Intestine Large	intestine
18	chr4:77178800-77201200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:77179000-77181400	Weak transcription	Liver	Liver
20	chr4:77179000-77186800	Weak transcription	Brain Substantia Nigra	brain
21	chr4:77179400-77185000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr4:77179400-77185400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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