Variant report

Variant	rs2277323
Chromosome Location	chr12:58009372-58009373
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57911754..57916322-chr12:58006406..58010716,5	K562	blood:
2	chr12:58007372..58011848-chr12:58013286..58019253,6	MCF-7	breast:
3	chr12:57911699..57918406-chr12:58000825..58010019,18	K562	blood:
4	chr12:57912181..57914315-chr12:58008996..58011925,2	MCF-7	breast:
5	chr12:58007718..58010411-chr12:58087376..58090012,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-B4GALNT1-1	chr12:58009275-58009435	ENSG00000224713.3

No data

Variant related genes	Relation type
ENSG00000135506	Chromatin interaction
ENSG00000135502	Chromatin interaction
ENSG00000224713	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000175197	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11172290	0.83[CEU][hapmap];0.83[CHB][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.88[TSI][hapmap]
rs11172314	1.00[ASW][hapmap]
rs12304013	0.83[EUR][1000 genomes]
rs12307841	1.00[ASW][hapmap]
rs12318458	0.81[EUR][1000 genomes]
rs12320537	0.85[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12322482	0.90[CEU][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2619468	0.82[CHD][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap]
rs35831868	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71432310	0.83[EUR][1000 genomes]
rs715930	0.90[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs774898	0.83[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs774899	0.83[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap]

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	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2277323	INHBE	cis	cerebellum	SCAN
rs2277323	XRCC6BP1	cis	multi-tissue	Pritchard
rs2277323	KRT77	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58005600-58011400	Weak transcription	Lung	lung
2	chr12:58005600-58013200	Weak transcription	Gastric	stomach
3	chr12:58006000-58010000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
4	chr12:58006200-58010000	Weak transcription	Brain Substantia Nigra	brain
5	chr12:58006200-58010200	Weak transcription	NHDF-Ad	bronchial
6	chr12:58006200-58010400	Weak transcription	NH-A	brain
7	chr12:58006200-58014800	Weak transcription	Brain Angular Gyrus	brain
8	chr12:58006400-58009400	Weak transcription	Brain Hippocampus Middle	brain
9	chr12:58006400-58011200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:58006600-58009400	Weak transcription	NHLF	lung
11	chr12:58006600-58010000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:58006600-58011000	Strong transcription	Fetal Lung	lung
13	chr12:58006600-58013200	Weak transcription	Pancreas	Pancrea
14	chr12:58006800-58010200	Weak transcription	Fetal Brain Male	brain
15	chr12:58006800-58011400	Strong transcription	Ovary	ovary
16	chr12:58006800-58011600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:58006800-58011600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:58006800-58011600	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:58006800-58011800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:58006800-58012000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:58007000-58009600	Genic enhancers	Fetal Muscle Leg	muscle
22	chr12:58007000-58012000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:58007200-58009400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:58007200-58009800	Strong transcription	Osteobl	bone
25	chr12:58007200-58011200	Strong transcription	Fetal Brain Female	brain
26	chr12:58007400-58009400	Enhancers	Primary B cells from cord blood	blood
27	chr12:58007400-58009600	Genic enhancers	Left Ventricle	heart
28	chr12:58007400-58010200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:58007600-58010000	Weak transcription	Esophagus	oesophagus
30	chr12:58007600-58010600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:58008000-58009400	Enhancers	Primary B cells from peripheral blood	blood
32	chr12:58008000-58009800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr12:58008000-58010800	Strong transcription	Brain Germinal Matrix	brain
34	chr12:58008000-58011400	Strong transcription	Fetal Stomach	stomach
35	chr12:58008000-58012800	Weak transcription	HepG2	liver
36	chr12:58008200-58009600	Genic enhancers	Rectal Smooth Muscle	rectum
37	chr12:58008200-58010000	Weak transcription	Right Atrium	heart
38	chr12:58008200-58010600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:58008400-58009600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:58008400-58010600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:58008400-58012000	Strong transcription	Aorta	Aorta
42	chr12:58008600-58009400	Weak transcription	Spleen	Spleen
43	chr12:58008600-58010000	Genic enhancers	Right Ventricle	heart
44	chr12:58008600-58010200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:58008600-58010400	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr12:58008600-58010400	Genic enhancers	Stomach Smooth Muscle	stomach
47	chr12:58009000-58010000	Weak transcription	K562	blood
48	chr12:58009000-58010200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr12:58009000-58010200	Strong transcription	Brain Cingulate Gyrus	brain
50	chr12:58009000-58010800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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