Variant report

Variant	rs2881925
Chromosome Location	chr2:20390694-20390695
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20306400..20314350-chr2:20385971..20392665,10	MCF-7	breast:
2	chr2:20304028..20306367-chr2:20390369..20392912,2	MCF-7	breast:
3	chr2:20389942..20391979-chr2:20394528..20396636,2	K562	blood:
4	chr2:20386118..20389028-chr2:20389700..20391555,2	K562	blood:

Variant related genes	Relation type
ENSG00000234378	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs4233759	0.85[AFR][1000 genomes]
rs7584270	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012841	chr2:20328894-20415168	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1007926	chr2:20350751-20393557	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2881925	RDH14	cis	cerebellum	SCAN
rs2881925	SDC1	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20384600-20391800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:20384600-20392000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:20384600-20400000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:20385200-20391800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:20385800-20391000	Weak transcription	Gastric	stomach
6	chr2:20386000-20391200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:20386200-20396000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:20386200-20401400	Weak transcription	Spleen	Spleen
9	chr2:20386400-20391000	Weak transcription	Pancreas	Pancrea
10	chr2:20386400-20395000	Enhancers	Liver	Liver
11	chr2:20386600-20396000	Weak transcription	Fetal Kidney	kidney
12	chr2:20386600-20401400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:20387200-20391800	Enhancers	Esophagus	oesophagus
14	chr2:20387400-20391000	Weak transcription	Colonic Mucosa	Colon
15	chr2:20387400-20391000	Weak transcription	Fetal Intestine Large	intestine
16	chr2:20387400-20391000	Weak transcription	Fetal Intestine Small	intestine
17	chr2:20387600-20395200	Enhancers	HepG2	liver
18	chr2:20388400-20392400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr2:20388600-20400400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:20388800-20391200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:20388800-20391800	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr2:20388800-20392200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr2:20389000-20391200	Weak transcription	Fetal Muscle Leg	muscle
24	chr2:20389000-20392600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:20389200-20390800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:20389200-20413600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr2:20389400-20390800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:20389400-20390800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:20389400-20390800	Weak transcription	A549	lung
30	chr2:20389400-20391200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:20389400-20398400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:20389600-20390800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:20389600-20390800	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr2:20389600-20391000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr2:20389600-20391000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:20389800-20390800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:20389800-20390800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:20389800-20397600	Weak transcription	Lung	lung
39	chr2:20389800-20400400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr2:20390000-20392600	Weak transcription	Placenta	Placenta
41	chr2:20390400-20396000	Weak transcription	NHEK	skin
42	chr2:20390600-20391600	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr2:20390600-20392000	Enhancers	Fetal Lung	lung
44	chr2:20390600-20392600	Enhancers	Duodenum Mucosa	Duodenum
45	chr2:20390600-20395200	Enhancers	Stomach Mucosa	stomach
46	chr2:20390600-20400200	Weak transcription	HMEC	breast

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