Variant report

Variant	rs6725478
Chromosome Location	chr2:234615400-234615401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:234386983..234399433-chr2:234613282..234621553,23	MCF-7	breast:
2	chr2:234610804..234613588-chr2:234613696..234615763,4	MCF-7	breast:
3	chr2:234614061..234616224-chr2:234620494..234622602,2	MCF-7	breast:
4	chr2:234597435..234606028-chr2:234613419..234620116,22	MCF-7	breast:
5	chr2:234614862..234617067-chr2:234739874..234742811,2	MCF-7	breast:
6	chr2:234599124..234606471-chr2:234613478..234621007,17	MCF-7	breast:
7	chr2:234393460..234398388-chr2:234612624..234620814,16	MCF-7	breast:
8	chr2:234614755..234617030-chr2:234761060..234764028,2	MCF-7	breast:
9	chr2:234591661..234593982-chr2:234613958..234615521,2	MCF-7	breast:
10	chr2:234429004..234430713-chr2:234613952..234615612,2	MCF-7	breast:
11	chr2:234613458..234615590-chr2:234762717..234764318,2	MCF-7	breast:
12	chr2:234613247..234615751-chr2:234736486..234739479,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000240224	Chromatin interaction
ENSG00000167165	Chromatin interaction
ENSG00000185038	Chromatin interaction
ENSG00000123485	Chromatin interaction
ENSG00000085982	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10167119	0.96[CEU][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs10168155	0.81[CEU][hapmap]
rs10168333	0.81[CEU][hapmap]
rs10171367	0.81[CEU][hapmap]
rs10175809	0.81[CEU][hapmap]
rs10178992	0.91[CEU][hapmap]
rs10179094	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs10180090	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10197460	0.96[CEU][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs10445704	0.81[CEU][hapmap]
rs11673726	0.91[CEU][hapmap]
rs11680450	0.81[CEU][hapmap]
rs11692021	0.80[EUR][1000 genomes]
rs11888459	0.91[CEU][hapmap]
rs11891311	0.91[CEU][hapmap];0.82[GIH][hapmap]
rs11902131	0.81[CEU][hapmap]
rs12623271	0.81[CEU][hapmap]
rs13002774	0.81[CEU][hapmap]
rs13015720	0.81[CEU][hapmap]
rs13401281	0.81[EUR][1000 genomes]
rs17863787	1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1875263	0.91[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.85[EUR][1000 genomes]
rs1983023	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2018985	1.00[CEU][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs3806592	0.85[EUR][1000 genomes]
rs4261716	0.81[CEU][hapmap]
rs4347832	0.81[CEU][hapmap]
rs4477910	0.85[EUR][1000 genomes]
rs4530361	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs4553819	0.81[CEU][hapmap]
rs6431625	0.83[EUR][1000 genomes]
rs6724485	0.81[CEU][hapmap]
rs6736508	0.81[CEU][hapmap]
rs6736743	0.81[CEU][hapmap]
rs6744284	0.81[CHD][hapmap];0.89[GIH][hapmap]
rs6749496	0.95[EUR][1000 genomes]
rs6753320	0.81[CEU][hapmap]
rs6753569	0.81[CEU][hapmap]
rs6759892	0.81[CEU][hapmap]
rs7563561	0.81[CEU][hapmap]
rs7564935	0.91[CEU][hapmap]
rs7567229	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7577677	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs7583278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap]
rs7586110	0.96[CEU][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs7604115	0.91[CEU][hapmap]
rs7608175	0.81[CEU][hapmap]
rs869283	1.00[CEU][hapmap];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv2760615	chr2:234613030-234640233	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6725478	EFHD1	cis	parietal	SCAN
rs6725478	EFHD1	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234611000-234616000	Enhancers	Liver	Liver
2	chr2:234611400-234616600	Weak transcription	HUVEC	blood vessel
3	chr2:234614000-234617400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:234614200-234616200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:234614200-234617000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:234614400-234615400	Flanking Active TSS	NHEK	skin
7	chr2:234614400-234615800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:234614400-234615800	Enhancers	Esophagus	oesophagus
9	chr2:234614400-234616000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr2:234614400-234618000	Enhancers	Stomach Mucosa	stomach
11	chr2:234614600-234615400	Enhancers	Pancreas	Pancrea
12	chr2:234614600-234615800	Enhancers	Placenta Amnion	Placenta Amnion
13	chr2:234614600-234615800	Enhancers	HMEC	breast
14	chr2:234614600-234616800	Enhancers	Hela-S3	cervix
15	chr2:234614800-234615600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:234614800-234615600	Enhancers	Fetal Intestine Large	intestine
17	chr2:234614800-234615600	Enhancers	HSMMtube	muscle
18	chr2:234614800-234617400	Enhancers	Osteobl	bone
19	chr2:234614800-234617800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:234615000-234615800	Enhancers	Duodenum Mucosa	Duodenum
21	chr2:234615000-234616000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:234615000-234617000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:234615000-234617400	Enhancers	NH-A	brain
24	chr2:234615000-234619800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:234615200-234615800	Enhancers	Gastric	stomach
26	chr2:234615200-234616000	Enhancers	A549	lung
27	chr2:234615200-234617000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr2:234615400-234615800	Enhancers	NHEK	skin
29	chr2:234615400-234620400	Weak transcription	Pancreas	Pancrea

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