Variant report

Variant	rs9399589
Chromosome Location	chr6:147200046-147200047
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:147199344..147201581-chr6:147203117..147205673,2	MCF-7	breast:
2	chr6:147199212..147201733-chr6:147207902..147209684,2	MCF-7	breast:
3	chr6:147198204..147200718-chr6:147295140..147296897,2	K562	blood:
4	chr6:147196025..147200245-chr6:147523517..147529134,7	K562	blood:

Variant related genes	Relation type
ENSG00000233452	Chromatin interaction
ENSG00000164506	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1998641	0.88[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs4895704	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs724774	0.81[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs912577	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9377035	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9390435	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9399590	0.88[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs9403825	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9403828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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	nsv830838	chr6:147090745-147274669	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:147193000-147200800	Weak transcription	Esophagus	oesophagus
2	chr6:147196800-147200800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr6:147196800-147202200	Enhancers	Primary hematopoietic stem cells	blood
4	chr6:147197000-147201400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr6:147197200-147200400	Enhancers	Fetal Intestine Small	intestine
6	chr6:147197200-147200800	Enhancers	Primary B cells from cord blood	blood
7	chr6:147197800-147200800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:147197800-147202200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:147198000-147203000	Weak transcription	Small Intestine	intestine
10	chr6:147198200-147200200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:147198200-147203600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:147198200-147205600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr6:147198400-147200600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:147198400-147201000	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr6:147198600-147200200	Enhancers	Liver	Liver
16	chr6:147198800-147202800	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr6:147199200-147200200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:147199200-147200400	Enhancers	Fetal Intestine Large	intestine
19	chr6:147199200-147200600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:147199200-147200800	Enhancers	Duodenum Mucosa	Duodenum
21	chr6:147199400-147201200	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr6:147199400-147202600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:147199600-147200200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:147199600-147200200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:147199600-147200200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr6:147199600-147200200	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr6:147199600-147200200	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr6:147199600-147200400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr6:147199600-147201400	Flanking Active TSS	K562	blood
30	chr6:147199800-147200200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:147199800-147200200	Enhancers	Fetal Kidney	kidney
32	chr6:147199800-147200200	Enhancers	Hela-S3	cervix
33	chr6:147199800-147200600	Enhancers	Stomach Mucosa	stomach
34	chr6:147200000-147205600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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