Variant report

Variant	rs10735877
Chromosome Location	chr12:59478920-59478921
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:59312732..59314963-chr12:59478479..59481283,2	MCF-7	breast:
2	chr12:59301019..59303651-chr12:59478405..59481329,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139263	Chromatin interaction
ENSG00000257443	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10506353	0.83[EUR][1000 genomes]
rs12423606	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1444089	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1444090	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17122093	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17618789	1.00[CHB][hapmap]
rs17628225	0.87[EUR][1000 genomes]
rs61934327	0.88[EUR][1000 genomes]
rs61934328	0.88[EUR][1000 genomes]
rs61934330	0.88[EUR][1000 genomes]
rs61934332	0.85[EUR][1000 genomes]
rs61934333	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7134004	0.94[EUR][1000 genomes]
rs907344	0.94[EUR][1000 genomes]
rs978615	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10735877	OR6C74	cis	parietal	SCAN
rs10735877	MARCH9	cis	parietal	SCAN
rs10735877	NDUFA4L2	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59468400-59489000	Weak transcription	Esophagus	oesophagus
2	chr12:59471800-59480000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:59476200-59479000	Enhancers	Fetal Intestine Large	intestine
4	chr12:59476200-59480400	Enhancers	Fetal Intestine Small	intestine
5	chr12:59477000-59479400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:59477000-59480200	Enhancers	Fetal Stomach	stomach
7	chr12:59477200-59480000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:59477400-59480800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:59477600-59479000	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr12:59477600-59479400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:59477600-59479600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:59477600-59479800	Enhancers	Rectal Smooth Muscle	rectum
13	chr12:59477600-59480600	Enhancers	Fetal Lung	lung
14	chr12:59477600-59480600	Enhancers	Stomach Mucosa	stomach
15	chr12:59477600-59480800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr12:59477600-59480800	Enhancers	Fetal Kidney	kidney
17	chr12:59477600-59480800	Enhancers	NHDF-Ad	bronchial
18	chr12:59477600-59480800	Enhancers	NHLF	lung
19	chr12:59477600-59481400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:59477800-59479000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:59477800-59479600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:59477800-59480600	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr12:59477800-59480600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr12:59477800-59480800	Enhancers	HMEC	breast
25	chr12:59478000-59479200	Enhancers	H9 Cell Line	embryonic stem cell
26	chr12:59478000-59479200	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr12:59478000-59479400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:59478000-59479400	Enhancers	HUVEC	blood vessel
29	chr12:59478000-59480600	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr12:59478000-59480800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:59478200-59479000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:59478200-59479600	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr12:59478200-59479800	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr12:59478200-59480400	Enhancers	Fetal Muscle Leg	muscle
35	chr12:59478200-59480600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:59478400-59479000	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr12:59478400-59479000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:59478400-59479000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:59478400-59479000	Enhancers	Osteobl	bone
40	chr12:59478400-59479400	Enhancers	NHEK	skin
41	chr12:59478600-59479000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:59478600-59479000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:59478600-59479000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:59478600-59479000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:59478600-59479000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr12:59478600-59479000	Enhancers	Fetal Muscle Trunk	muscle
47	chr12:59478600-59479000	Enhancers	Ovary	ovary
48	chr12:59478600-59479000	Flanking Active TSS	NH-A	brain
49	chr12:59478600-59479200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:59478600-59479200	Active TSS	Aorta	Aorta

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