Variant report

Variant	rs17425839
Chromosome Location	chr7:106763278-106763279
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:106595488..106597502-chr7:106762863..106765295,2	K562	blood:
2	chr7:106758338..106764919-chr7:106770335..106778369,9	K562	blood:
3	chr7:106755457..106758160-chr7:106760094..106763600,5	K562	blood:
4	chr7:106759524..106761230-chr7:106763085..106765571,2	K562	blood:
5	chr7:106761889..106764464-chr7:106771416..106774166,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243193	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1004570	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10232542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10241141	0.91[ASN][1000 genomes]
rs10241155	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10248105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10249866	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10261881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10271426	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10272371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11509187	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11760966	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11762123	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11764389	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11766060	1.00[LWK][hapmap]
rs11767753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11772066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12055946	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12154324	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17153823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17153861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17340358	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17340479	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17340577	1.00[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17341680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17349904	1.00[LWK][hapmap]
rs17424512	0.83[EUR][1000 genomes]
rs17424561	1.00[ASW][hapmap]
rs1860804	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1860805	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1981696	1.00[CHD][hapmap]
rs2041525	0.88[EUR][1000 genomes]
rs2041526	0.88[EUR][1000 genomes]
rs2191917	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2536490	0.80[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs257377	1.00[ASW][hapmap];0.88[CHD][hapmap]
rs257387	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap]
rs28610544	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28873708	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3729876	1.00[CHD][hapmap]
rs3729877	0.88[CHD][hapmap]
rs3752645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3779500	1.00[CHD][hapmap]
rs4460293	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56704102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58386564	0.88[EUR][1000 genomes]
rs58979869	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6946036	1.00[LWK][hapmap]
rs6946931	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap]
rs6960708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6971393	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6971774	1.00[ASW][hapmap]
rs6978486	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7778076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7780728	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7780784	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7780830	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7786296	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7786692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7794915	1.00[LWK][hapmap]
rs8180787	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9641372	0.84[EUR][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	nsv831087	chr7:106673465-106872460	Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:106756600-106771200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr7:106759800-106763400	Weak transcription	NHLF	lung
3	chr7:106759800-106771600	Weak transcription	Brain Anterior Caudate	brain
4	chr7:106759800-106774000	Weak transcription	Left Ventricle	heart
5	chr7:106760200-106763400	Weak transcription	Fetal Stomach	stomach
6	chr7:106760200-106771200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr7:106760200-106782000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr7:106760400-106808400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:106760600-106765400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr7:106760600-106771400	Weak transcription	Fetal Kidney	kidney
11	chr7:106762000-106763800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr7:106762200-106763400	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr7:106762200-106765800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr7:106762400-106763400	Enhancers	Liver	Liver
15	chr7:106762600-106763400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr7:106762600-106763400	Enhancers	Muscle Satellite Cultured Cells	--
17	chr7:106762600-106763600	Enhancers	Adipose Nuclei	Adipose
18	chr7:106762600-106763600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr7:106762800-106763400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr7:106762800-106763400	Active TSS	Ovary	ovary
21	chr7:106762800-106764200	Enhancers	Fetal Lung	lung
22	chr7:106762800-106764400	Strong transcription	K562	blood
23	chr7:106763000-106763600	Enhancers	A549	lung
24	chr7:106763000-106807800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr7:106763200-106764400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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