Variant report

Variant	rs7952875
Chromosome Location	chr12:59507893-59507894
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:59507288..59508240-chr12:61932726..61933441,2	MCF-7	breast:
2	chr12:59507135..59508358-chr12:59543262..59544671,18	MCF-7	breast:
3	chr12:59507415..59508147-chr12:59543545..59544473,6	MCF-7	breast:
4	chr12:59507585..59508107-chr12:59766521..59767200,2	MCF-7	breast:
5	chr12:59506961..59508922-chr12:59510527..59512982,3	MCF-7	breast:
6	chr12:58934011..58934535-chr12:59507466..59507984,2	MCF-7	breast:
7	chr12:59507468..59508144-chr12:59801341..59801884,3	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1023797	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172909	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12367511	0.90[EUR][1000 genomes]
rs1500033	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1500034	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17628272	0.90[EUR][1000 genomes]
rs1846623	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1846624	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36082506	0.83[EUR][1000 genomes]
rs6581231	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6581232	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7136863	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7953477	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957634	0.88[EUR][1000 genomes]
rs908394	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1047257	chr12:59444966-59520330	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1050662	chr12:59444966-59526442	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv469412	chr12:59504600-59542117	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv559051	chr12:59504600-59542117	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7952875	RDH5	cis	cerebellum	SCAN
rs7952875	DDIT3	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59497200-59513400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr12:59501200-59513200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:59506000-59517400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:59506200-59508000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:59506200-59509400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr12:59507400-59508200	Enhancers	Dnd41	blood
7	chr12:59507800-59508000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:59507800-59508000	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr12:59507800-59508000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:59507800-59508000	Enhancers	Brain Angular Gyrus	brain
11	chr12:59507800-59508000	Enhancers	Brain Cingulate Gyrus	brain
12	chr12:59507800-59508000	Enhancers	Duodenum Mucosa	Duodenum
13	chr12:59507800-59508000	Enhancers	Rectal Smooth Muscle	rectum
14	chr12:59507800-59508200	Enhancers	H1 Cell Line	embryonic stem cell
15	chr12:59507800-59508200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:59507800-59508200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:59507800-59508200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:59507800-59508200	Enhancers	Adipose Nuclei	Adipose
19	chr12:59507800-59508200	Flanking Active TSS	Brain Anterior Caudate	brain
20	chr12:59507800-59508200	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr12:59507800-59508200	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr12:59507800-59508200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:59507800-59508200	Flanking Active TSS	Brain Substantia Nigra	brain
24	chr12:59507800-59508200	Enhancers	Esophagus	oesophagus
25	chr12:59507800-59508200	Enhancers	Fetal Brain Female	brain
26	chr12:59507800-59508200	Enhancers	Fetal Lung	lung
27	chr12:59507800-59508200	Enhancers	Fetal Muscle Trunk	muscle
28	chr12:59507800-59508200	Enhancers	Fetal Muscle Leg	muscle
29	chr12:59507800-59508200	Enhancers	Pancreas	Pancrea
30	chr12:59507800-59508200	Enhancers	Right Atrium	heart
31	chr12:59507800-59508200	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr12:59507800-59508200	Enhancers	Stomach Mucosa	stomach
33	chr12:59507800-59508200	Flanking Active TSS	Stomach Smooth Muscle	stomach
34	chr12:59507800-59508200	Flanking Active TSS	HepG2	liver
35	chr12:59507800-59508400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:59507800-59508400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:59507800-59508400	Enhancers	Fetal Intestine Small	intestine
38	chr12:59507800-59508400	Enhancers	Fetal Stomach	stomach
39	chr12:59507800-59508600	Enhancers	Colon Smooth Muscle	Colon
40	chr12:59507800-59508800	Enhancers	Fetal Intestine Large	intestine
41	chr12:59507800-59509400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:59507800-59509800	Enhancers	NHDF-Ad	bronchial
43	chr12:59507800-59510000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:59507800-59510000	Enhancers	HUVEC	blood vessel
45	chr12:59507800-59510200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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