Variant report

Variant	rs6988293
Chromosome Location	chr8:121234298-121234299
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:121233564..121236252-chr8:121236921..121239652,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10808508	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs10955962	0.87[EUR][1000 genomes]
rs11773991	0.92[CEU][hapmap];0.81[TSI][hapmap];0.91[EUR][1000 genomes]
rs12542144	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs12543412	0.91[EUR][1000 genomes]
rs12547117	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs12679689	0.81[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap]
rs13258640	0.80[CEU][hapmap]
rs13258857	0.81[CEU][hapmap]
rs2034841	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs2034842	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs2054148	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs2219246	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs2290519	0.81[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap]
rs2305597	0.94[ASW][hapmap];0.80[JPT][hapmap];0.83[YRI][hapmap];0.81[ASN][1000 genomes]
rs2305598	0.88[CEU][hapmap]
rs2305600	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2305604	0.81[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap]
rs2875940	0.80[EUR][1000 genomes]
rs35784860	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765062	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs4870722	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4870723	0.89[CEU][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs4870724	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs56159702	0.91[EUR][1000 genomes]
rs58829748	0.91[EUR][1000 genomes]
rs59767583	0.82[ASN][1000 genomes]
rs6989074	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs6994973	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6996780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7004406	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs7013555	0.88[CEU][hapmap]
rs7015242	0.82[ASN][1000 genomes]
rs7018223	0.94[ASW][hapmap];0.80[JPT][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs7018328	0.88[CEU][hapmap]
rs7387094	0.89[EUR][1000 genomes]
rs7387373	0.92[CEU][hapmap];0.81[TSI][hapmap];0.91[EUR][1000 genomes]
rs7842055	0.89[GIH][hapmap];0.83[MEX][hapmap]
rs921861	0.88[EUR][1000 genomes]
rs957694	0.86[EUR][1000 genomes]
rs957695	0.86[EUR][1000 genomes]
rs957696	0.92[CEU][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891418	chr8:120600965-121301474	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	esv3348294	chr8:121000288-121250984	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv891420	chr8:121194900-121561369	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv612112	chr8:121234298-121385167	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6988293	KLHL38	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:121214200-121253400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr8:121215200-121260600	Weak transcription	Fetal Intestine Small	intestine
3	chr8:121217200-121261600	Weak transcription	Fetal Intestine Large	intestine
4	chr8:121217400-121234400	Weak transcription	Fetal Muscle Leg	muscle
5	chr8:121222200-121255200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr8:121224800-121243800	Weak transcription	Placenta	Placenta
7	chr8:121229600-121249000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr8:121231200-121238800	Weak transcription	Aorta	Aorta
9	chr8:121232000-121234600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr8:121232000-121234600	Weak transcription	Fetal Stomach	stomach
11	chr8:121233000-121234800	Enhancers	Adipose Nuclei	Adipose
12	chr8:121233000-121235000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr8:121233000-121235200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr8:121233400-121234400	Weak transcription	Fetal Lung	lung
15	chr8:121233400-121234400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr8:121233400-121242200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr8:121233600-121238600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr8:121234000-121239400	Weak transcription	Ovary	ovary
19	chr8:121234000-121239600	Weak transcription	Osteobl	bone
20	chr8:121234200-121236800	Weak transcription	Colon Smooth Muscle	Colon
21	chr8:121234200-121238800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr8:121234200-121240200	Weak transcription	Stomach Smooth Muscle	stomach

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