Variant report

Variant	rs9389988
Chromosome Location	chr6:142684501-142684502
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:142683592..142686831-chr6:142690528..142693685,3	MCF-7	breast:
2	chr6:142621912..142626098-chr6:142682605..142686113,5	MCF-7	breast:
3	chr6:142683303..142685618-chr6:142695779..142698326,2	MCF-7	breast:
4	chr6:142622374..142624698-chr6:142682481..142685205,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NMBR-5	chr6:142684212-142686824	NONHSAT115311

Variant related genes	Relation type
ENSG00000112414	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1013902	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17071798	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2064314	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2143390	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2223616	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294765	0.82[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2294768	0.82[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2294770	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2294772	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2294773	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2294774	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34701089	0.86[EUR][1000 genomes]
rs41289839	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4140531	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6570512	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6913116	0.82[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7758750	0.82[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7759268	0.82[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9321865	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9321871	0.83[EUR][1000 genomes]
rs9373343	0.82[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9373345	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9376687	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9376689	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9385993	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9385994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9389990	0.82[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9403379	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9403384	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9484645	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142676800-142688600	Weak transcription	Fetal Heart	heart
2	chr6:142679400-142684800	Weak transcription	Fetal Brain Female	brain
3	chr6:142679400-142688200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:142679400-142693200	Weak transcription	Hela-S3	cervix
5	chr6:142681000-142695200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:142682600-142694600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:142682800-142693600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:142682800-142694600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:142683200-142693400	Weak transcription	HSMM	muscle
10	chr6:142683400-142693800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:142683600-142684600	Weak transcription	Osteobl	bone
12	chr6:142683600-142684800	Weak transcription	Fetal Brain Male	brain
13	chr6:142683600-142693200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:142683800-142687400	Weak transcription	Fetal Lung	lung
15	chr6:142683800-142688200	Enhancers	A549	lung
16	chr6:142683800-142688600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:142683800-142688600	Weak transcription	NHLF	lung
18	chr6:142683800-142691400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:142683800-142693200	Weak transcription	HMEC	breast
20	chr6:142683800-142693400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:142683800-142693400	Weak transcription	Fetal Intestine Large	intestine
22	chr6:142683800-142693400	Weak transcription	Fetal Intestine Small	intestine
23	chr6:142683800-142693600	Weak transcription	Placenta	Placenta
24	chr6:142684000-142686200	Weak transcription	HepG2	liver
25	chr6:142684000-142688800	Weak transcription	HUVEC	blood vessel
26	chr6:142684000-142689400	Weak transcription	Liver	Liver
27	chr6:142684000-142691400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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