Variant report

Variant	rs3800404
Chromosome Location	chr6:35137870-35137871
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:35127079..35138793-chr6:35145525..35157743,32	MCF-7	breast:
2	chr6:35136063..35139125-chr6:35139498..35141793,3	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1408255	0.82[ASN][1000 genomes]
rs2005	0.80[JPT][hapmap]
rs3800403	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3800405	0.82[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4711405	0.89[ASN][1000 genomes]
rs4711407	0.85[ASN][1000 genomes]
rs6457801	0.85[ASN][1000 genomes]
rs6457802	0.85[ASN][1000 genomes]
rs6457804	0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6457806	0.87[CEU][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs6911268	0.85[ASN][1000 genomes]
rs6914081	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs6920194	0.81[ASN][1000 genomes]
rs6925406	0.85[ASN][1000 genomes]
rs6931790	0.85[ASN][1000 genomes]
rs6939132	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7772251	0.83[JPT][hapmap]
rs9366881	0.85[EUR][1000 genomes]
rs9380494	0.85[ASN][1000 genomes]
rs9380495	0.83[ASN][1000 genomes]
rs9394277	0.82[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9394287	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs942373	0.82[CEU][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs942374	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs942375	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[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	esv3340708	chr6:35135274-35139572	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3800404	UHRF1BP1	cis	parietal	SCAN
rs3800404	C6orf227	cis	cerebellum	SCAN
rs3800404	GRM4	cis	cerebellum	SCAN
rs3800404	C6orf106	cis	cerebellum	SCAN
rs3800404	GLO1	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35130600-35141400	Weak transcription	Brain Substantia Nigra	brain
2	chr6:35134400-35140400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:35135000-35148800	Weak transcription	Esophagus	oesophagus
4	chr6:35135600-35138600	Weak transcription	Stomach Mucosa	stomach
5	chr6:35136600-35139400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:35136600-35139600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:35137000-35141600	Weak transcription	Fetal Heart	heart
8	chr6:35137000-35141600	Weak transcription	Left Ventricle	heart
9	chr6:35137000-35148800	Weak transcription	Right Atrium	heart
10	chr6:35137200-35139600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:35137400-35139200	Enhancers	NH-A	brain
12	chr6:35137400-35139600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:35137400-35139600	Enhancers	NHDF-Ad	bronchial
14	chr6:35137400-35139800	Enhancers	Muscle Satellite Cultured Cells	--
15	chr6:35137400-35142200	Enhancers	Osteobl	bone
16	chr6:35137600-35138000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:35137600-35138000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:35137600-35138000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:35137600-35139000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:35137600-35139000	Enhancers	NHLF	lung
21	chr6:35137600-35140800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr6:35137600-35141200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:35137600-35141600	Weak transcription	Brain Angular Gyrus	brain
24	chr6:35137600-35145200	Weak transcription	Fetal Kidney	kidney
25	chr6:35137800-35138000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:35137800-35138400	Enhancers	HSMM	muscle
27	chr6:35137800-35139000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:35137800-35141000	Weak transcription	H1 Cell Line	embryonic stem cell

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