Variant report

Variant	rs2043258
Chromosome Location	chr2:56236566-56236567
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55998478..55999313-chr2:56236137..56237588,8	MCF-7	breast:
2	chr2:56234512..56236770-chr2:56238872..56240573,2	K562	blood:

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10210936	0.97[AFR][1000 genomes]
rs12713313	0.91[AFR][1000 genomes]
rs12713314	0.91[AFR][1000 genomes]
rs4553860	0.89[AFR][1000 genomes]
rs7587002	0.98[AFR][1000 genomes]
rs7597360	0.97[AFR][1000 genomes]

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	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv2757799	chr2:56178439-56472394	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	esv2759051	chr2:56178439-56472394	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
4	nsv520175	chr2:56228351-56331375	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2043258	CCDC88A	cis	cerebellum	SCAN
rs2043258	C2orf63	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56234800-56242800	Enhancers	HUVEC	blood vessel
2	chr2:56235200-56237000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:56235400-56236600	Enhancers	Brain Substantia Nigra	brain
4	chr2:56235400-56236600	Enhancers	Fetal Stomach	stomach
5	chr2:56235400-56236800	Enhancers	Brain Angular Gyrus	brain
6	chr2:56235400-56237000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:56235400-56237000	Enhancers	HSMM	muscle
8	chr2:56235400-56237000	Enhancers	Osteobl	bone
9	chr2:56235600-56236800	Enhancers	Fetal Lung	lung
10	chr2:56235600-56237000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:56235600-56237000	Enhancers	NHLF	lung
12	chr2:56235600-56237600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:56235600-56238600	Enhancers	Fetal Kidney	kidney
14	chr2:56235800-56236600	Enhancers	Fetal Muscle Leg	muscle
15	chr2:56235800-56238600	Enhancers	Fetal Intestine Small	intestine
16	chr2:56236000-56236600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:56236000-56236600	Enhancers	Adipose Nuclei	Adipose
18	chr2:56236000-56236600	Flanking Active TSS	Brain Germinal Matrix	brain
19	chr2:56236000-56236600	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr2:56236000-56236600	Enhancers	Right Atrium	heart
21	chr2:56236000-56236600	Flanking Active TSS	HSMMtube	muscle
22	chr2:56236000-56236800	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr2:56236000-56236800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:56236000-56237000	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr2:56236000-56237000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:56236000-56237000	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr2:56236000-56237000	Enhancers	Fetal Intestine Large	intestine
28	chr2:56236000-56237000	Enhancers	NHDF-Ad	bronchial
29	chr2:56236000-56237400	Enhancers	A549	lung
30	chr2:56236000-56237600	Enhancers	Hela-S3	cervix
31	chr2:56236200-56236600	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr2:56236200-56236600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:56236200-56236600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:56236200-56236600	Active TSS	Fetal Brain Female	brain
35	chr2:56236200-56236600	Flanking Active TSS	Ovary	ovary
36	chr2:56236200-56236800	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr2:56236200-56236800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:56236200-56237000	Active TSS	Brain Anterior Caudate	brain
39	chr2:56236400-56236600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:56236400-56236600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr2:56236400-56236600	Enhancers	NH-A	brain
42	chr2:56236400-56236800	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr2:56236400-56236800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr2:56236400-56236800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:56236400-56236800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:56236400-56236800	Active TSS	Brain Cingulate Gyrus	brain
47	chr2:56236400-56237000	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr2:56236400-56237000	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr2:56236400-56237000	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr2:56236400-56237000	Active TSS	Brain Hippocampus Middle	brain

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