Variant report

Variant	rs11752102
Chromosome Location	chr6:25154396-25154397
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:25154053..25159519-chr6:25164374..25167875,7	MCF-7	breast:
2	chr6:25151401..25154186-chr6:25154333..25156125,2	MCF-7	breast:
3	chr6:25150825..25153623-chr6:25154043..25156150,2	K562	blood:

Variant related genes	Relation type
ENSG00000168405	Chromatin interaction
ENSG00000262400	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10946752	0.88[ASN][1000 genomes]
rs12663706	0.84[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16890179	0.90[CEU][hapmap];0.85[JPT][hapmap]
rs1900554	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4712889	0.99[ASN][1000 genomes]
rs6909903	0.82[ASN][1000 genomes]
rs6910965	0.82[CEU][hapmap]
rs6915489	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6922783	0.90[ASN][1000 genomes]
rs6941417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748381	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9348664	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9356963	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9356964	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9366606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9379723	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9379726	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9393620	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9393621	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9461115	0.83[ASN][1000 genomes]
rs9467430	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv470806	chr6:25082262-25156197	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv462662	chr6:25084718-25165486	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv601166	chr6:25084718-25165486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv1020774	chr6:25154152-25285679	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv538161	chr6:25154152-25285679	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11752102	CMAH	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25139200-25154800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:25143400-25154600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:25150200-25155200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:25150400-25155400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:25150600-25155000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:25151200-25155600	Weak transcription	Right Atrium	heart
7	chr6:25152600-25155200	Genic enhancers	Dnd41	blood
8	chr6:25152800-25154400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
9	chr6:25153000-25156200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr6:25153000-25158000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr6:25153200-25155400	Weak transcription	Lung	lung
12	chr6:25153400-25155000	Enhancers	Pancreas	Pancrea
13	chr6:25153600-25154600	Weak transcription	Thymus	Thymus
14	chr6:25153600-25155600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:25153800-25155000	Enhancers	Fetal Kidney	kidney
16	chr6:25154000-25154400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr6:25154000-25154400	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr6:25154000-25156600	Genic enhancers	Fetal Thymus	thymus
19	chr6:25154000-25157600	Enhancers	Placenta	Placenta
20	chr6:25154200-25154400	Enhancers	Esophagus	oesophagus
21	chr6:25154200-25154600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:25154200-25155000	Enhancers	Fetal Intestine Large	intestine
23	chr6:25154200-25155000	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr6:25154200-25155600	Enhancers	Fetal Intestine Small	intestine
25	chr6:25154200-25155800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:25154200-25155800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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