Variant report

Variant	rs2291800
Chromosome Location	chr12:59307299-59307300
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:59270433..59273338-chr12:59306746..59309338,2	MCF-7	breast:
2	chr12:59306615..59312160-chr12:59312563..59315284,9	MCF-7	breast:
3	chr12:59305986..59308290-chr12:59311470..59314122,2	K562	blood:

Variant related genes	Relation type
ENSG00000139263	Chromatin interaction
ENSG00000257443	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10783927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877184	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs10877186	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs11172820	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11834094	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12301978	0.81[YRI][hapmap]
rs12426955	0.81[CHB][hapmap]
rs2291799	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7135114	0.81[CHD][hapmap];0.88[JPT][hapmap]
rs7303924	0.82[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	esv2758311	chr12:59022729-59323045	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2759902	chr12:59022729-59323045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2291800	RBMS2	cis	parietal	SCAN
rs2291800	MUCL1	cis	parietal	SCAN
rs2291800	MBD6	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59266000-59311000	Weak transcription	Fetal Thymus	thymus
2	chr12:59279000-59310800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr12:59279200-59309400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr12:59290600-59311000	Weak transcription	Right Ventricle	heart
5	chr12:59292400-59309200	Weak transcription	Fetal Heart	heart
6	chr12:59292400-59310600	Weak transcription	Small Intestine	intestine
7	chr12:59297800-59307400	Strong transcription	Fetal Intestine Large	intestine
8	chr12:59297800-59307600	Strong transcription	Duodenum Mucosa	Duodenum
9	chr12:59297800-59307600	Strong transcription	Fetal Muscle Trunk	muscle
10	chr12:59297800-59308000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:59297800-59308000	Strong transcription	NHDF-Ad	bronchial
12	chr12:59298600-59307800	Strong transcription	NHLF	lung
13	chr12:59300400-59307600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:59300800-59307600	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr12:59301200-59309400	Weak transcription	GM12878-XiMat	blood
16	chr12:59302000-59313000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:59302200-59309200	Weak transcription	Ovary	ovary
18	chr12:59302400-59308200	Weak transcription	Aorta	Aorta
19	chr12:59302400-59309000	Weak transcription	A549	lung
20	chr12:59302800-59309400	Weak transcription	Pancreas	Pancrea
21	chr12:59302800-59309600	Weak transcription	Colonic Mucosa	Colon
22	chr12:59303000-59307800	Strong transcription	Fetal Muscle Leg	muscle
23	chr12:59303200-59313400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:59303400-59308000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:59303800-59307600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:59303800-59307800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:59303800-59308200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr12:59303800-59309400	Weak transcription	Esophagus	oesophagus
29	chr12:59303800-59311800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:59303800-59312400	Weak transcription	Gastric	stomach
31	chr12:59303800-59313000	Weak transcription	Lung	lung
32	chr12:59304000-59307400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr12:59304000-59308200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:59304800-59308000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:59304800-59312800	Weak transcription	Placenta	Placenta
36	chr12:59305000-59307800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:59305000-59308800	Weak transcription	Brain Anterior Caudate	brain
38	chr12:59305000-59309200	Weak transcription	Brain Angular Gyrus	brain
39	chr12:59305000-59309400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:59305200-59308200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr12:59305200-59308400	Weak transcription	Brain Substantia Nigra	brain
42	chr12:59305200-59309200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr12:59305200-59309400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:59305200-59309400	Weak transcription	Psoas Muscle	Psoas
45	chr12:59305200-59309600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:59305200-59310600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr12:59305600-59307800	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr12:59305800-59307800	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr12:59305800-59307800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr12:59305800-59308800	Enhancers	Stomach Mucosa	stomach

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