Variant report

Variant	rs1341597
Chromosome Location	chr6:128779158-128779159
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:128778610..128780659-chr6:128782620..128784185,2	MCF-7	breast:
2	chr6:128773075..128776512-chr6:128778434..128782134,3	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10872330	1.00[MEX][hapmap]
rs12332836	1.00[EUR][1000 genomes]
rs12717181	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13196790	1.00[CEU][hapmap]
rs13216847	1.00[CEU][hapmap]
rs1341598	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1341599	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1891150	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs28531950	1.00[EUR][1000 genomes]
rs61143917	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71568904	0.82[EUR][1000 genomes]
rs7775722	1.00[EUR][1000 genomes]
rs8180639	1.00[MEX][hapmap]
rs9482890	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9491950	1.00[CEU][hapmap];0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs9491951	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9491964	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9491970	1.00[CEU][hapmap]
rs9491971	1.00[CEU][hapmap]
rs9491972	1.00[CEU][hapmap]
rs981999	1.00[MEX][hapmap]

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	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv830800	chr6:128710631-128878435	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1341597	S100A12	trans	brain	seeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128759800-128786800	Weak transcription	Left Ventricle	heart
2	chr6:128767800-128785200	Weak transcription	NHEK	skin
3	chr6:128768200-128785000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:128773400-128795200	Weak transcription	HSMMtube	muscle
5	chr6:128774600-128786800	Weak transcription	Right Ventricle	heart
6	chr6:128775200-128785800	Weak transcription	Ovary	ovary
7	chr6:128775400-128781000	Weak transcription	Pancreas	Pancrea
8	chr6:128775400-128785000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:128776600-128779400	Enhancers	Brain Anterior Caudate	brain
10	chr6:128776800-128780200	Enhancers	Brain Substantia Nigra	brain
11	chr6:128777000-128779400	Enhancers	HepG2	liver
12	chr6:128777000-128780200	Enhancers	Brain Angular Gyrus	brain
13	chr6:128777200-128785000	Weak transcription	Osteobl	bone
14	chr6:128777800-128782800	Weak transcription	Fetal Lung	lung
15	chr6:128777800-128786800	Weak transcription	Stomach Mucosa	stomach
16	chr6:128778000-128786800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:128778200-128781200	Weak transcription	Fetal Intestine Small	intestine
18	chr6:128778200-128782400	Weak transcription	Liver	Liver
19	chr6:128778200-128786200	Weak transcription	Fetal Intestine Large	intestine
20	chr6:128778400-128779200	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr6:128778400-128780800	Enhancers	Brain Hippocampus Middle	brain
22	chr6:128778600-128779400	Enhancers	Brain Cingulate Gyrus	brain
23	chr6:128778800-128779400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:128778800-128790600	Weak transcription	Fetal Heart	heart

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