Variant report

Variant	rs9401130
Chromosome Location	chr6:119470754-119470755
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr6:119469285-119470944	SK-N-SH	brain:	n/a	chr6:119469630-119469642 chr6:119469880-119469899
2	SMC3	chr6:119469261-119471467	SK-N-SH	brain:	n/a	chr6:119469881-119469895

No.	Distal block	Cell Line	Cell type
1	chr6:119256106..119257947-chr6:119468580..119471034,2	K562	blood:
2	chr6:119470751..119473289-chr6:119476279..119478742,2	MCF-7	breast:
3	chr6:119467858..119470789-chr6:119668770..119672252,3	K562	blood:
4	chr6:119214272..119216553-chr6:119469883..119471782,2	K562	blood:
5	chr6:119284318..119286217-chr6:119469822..119472613,2	K562	blood:

Variant related genes	Relation type
FAM184A	TF binding region
ENSG00000111879	Chromatin interaction
ENSG00000111885	Chromatin interaction
ENSG00000111877	Chromatin interaction
ENSG00000111875	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12190611	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1891540	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs608541	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs611211	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs624829	0.88[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs638368	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs656012	0.96[CEU][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes]
rs666655	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs678974	0.86[EUR][1000 genomes]
rs682949	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs683488	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6910397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6928078	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6934752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6935092	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs733259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs733260	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7775389	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];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9387637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9398502	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9398503	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9401129	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv886570	chr6:119450888-119600556	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1017507	chr6:119465981-119664949	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119457000-119474800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:119467800-119470800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr6:119467800-119470800	Enhancers	HMEC	breast
4	chr6:119468600-119470800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:119468800-119470800	Enhancers	Pancreas	Pancrea
6	chr6:119469000-119472200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:119469600-119471000	Enhancers	K562	blood
8	chr6:119469800-119470800	Enhancers	Muscle Satellite Cultured Cells	--
9	chr6:119469800-119472200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:119469800-119472200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:119469800-119476800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:119470200-119470800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:119470200-119472400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:119470200-119482400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:119470400-119470800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:119470400-119470800	Enhancers	NHEK	skin
17	chr6:119470400-119471000	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr6:119470400-119471000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:119470400-119471000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:119470400-119471200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:119470600-119470800	Enhancers	Osteobl	bone
22	chr6:119470600-119471000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:119470600-119471000	Enhancers	NH-A	brain
24	chr6:119470600-119471200	Enhancers	NHDF-Ad	bronchial
25	chr6:119470600-119471600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:119470600-119473800	Weak transcription	HepG2	liver

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