Variant report

Variant	rs2272249
Chromosome Location	chr2:54053476-54053477
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:62609118..62609651-chr2:54053034..54053551,3	Hela-S3	cervix:
2	chr10:103124609..103125127-chr2:54053027..54053548,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000222414	Chromatin interaction
ENSG00000133316	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10185375	0.85[JPT][hapmap]
rs10190578	0.87[CHD][hapmap]
rs10210726	0.85[JPT][hapmap]
rs12612589	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12613682	0.85[JPT][hapmap]
rs12617668	0.80[ASN][1000 genomes]
rs12618276	0.84[ASN][1000 genomes]
rs12618587	0.89[ASN][1000 genomes]
rs12620190	0.84[ASN][1000 genomes]
rs12620208	0.84[ASN][1000 genomes]
rs12621635	0.84[CHD][hapmap];0.85[JPT][hapmap]
rs17045125	1.00[JPT][hapmap]
rs17045215	0.85[JPT][hapmap]
rs17045292	0.86[ASN][1000 genomes]
rs2272250	0.96[ASN][1000 genomes]
rs2287344	0.94[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2287345	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2357491	0.84[CHD][hapmap];0.86[JPT][hapmap]
rs35819225	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3755120	0.84[CHD][hapmap]
rs3770389	1.00[YRI][hapmap]
rs3770401	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs3770415	0.82[JPT][hapmap]
rs3821080	0.87[CHD][hapmap]
rs3861570	0.80[ASN][1000 genomes]
rs6712204	0.81[CHD][hapmap]
rs72799229	0.92[ASN][1000 genomes]
rs72799234	0.92[ASN][1000 genomes]
rs72799235	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72799236	0.86[ASN][1000 genomes]
rs7595713	0.85[JPT][hapmap]
rs7595816	0.87[CHD][hapmap];0.81[GIH][hapmap]
rs7600276	0.84[ASN][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	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2272249	C2orf30	cis	normal skin	skin_eQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54015200-54053800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:54015600-54054600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:54015800-54054000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:54023000-54053800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:54025800-54062000	Weak transcription	Right Ventricle	heart
6	chr2:54025800-54085600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:54030400-54063000	Weak transcription	Esophagus	oesophagus
8	chr2:54040200-54055000	Weak transcription	Fetal Heart	heart
9	chr2:54041400-54054600	Weak transcription	Psoas Muscle	Psoas
10	chr2:54041400-54056400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:54042800-54062200	Weak transcription	Fetal Kidney	kidney
12	chr2:54043000-54053800	Weak transcription	NHEK	skin
13	chr2:54043200-54053800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:54043400-54053600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr2:54046000-54053600	Weak transcription	NH-A	brain
16	chr2:54046600-54080200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:54046600-54080200	Weak transcription	NHDF-Ad	bronchial
18	chr2:54046800-54054000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:54046800-54054200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:54046800-54054200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:54046800-54056800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr2:54046800-54060400	Weak transcription	Primary B cells from cord blood	blood
23	chr2:54046800-54070800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:54046800-54080400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:54047000-54053800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:54047000-54054000	Weak transcription	NHLF	lung
27	chr2:54047000-54056600	Weak transcription	Brain Germinal Matrix	brain
28	chr2:54047000-54060600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr2:54047000-54061400	Weak transcription	Fetal Thymus	thymus
30	chr2:54047000-54080200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr2:54047000-54080200	Weak transcription	A549	lung
32	chr2:54047000-54080400	Weak transcription	Gastric	stomach
33	chr2:54047000-54080400	Weak transcription	Pancreas	Pancrea
34	chr2:54047000-54080800	Weak transcription	Aorta	Aorta
35	chr2:54047200-54053800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:54047200-54053800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:54047200-54054000	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr2:54047200-54054200	Weak transcription	Left Ventricle	heart
39	chr2:54047200-54054600	Weak transcription	Lung	lung
40	chr2:54047200-54055200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:54047200-54056800	Weak transcription	HSMMtube	muscle
42	chr2:54047200-54059600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:54047200-54061800	Weak transcription	Thymus	Thymus
44	chr2:54047200-54063000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:54047200-54067600	Weak transcription	HSMM	muscle
46	chr2:54047200-54070800	Weak transcription	Placenta	Placenta
47	chr2:54047200-54077000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:54047200-54080000	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr2:54047200-54080200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:54047200-54080200	Weak transcription	Muscle Satellite Cultured Cells	--

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