Variant report

Variant	rs4420737
Chromosome Location	chr2:55422013-55422014
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55276244..55278085-chr2:55420013..55422421,2	K562	blood:
2	chr2:55421052..55423867-chr2:55459760..55462720,2	K562	blood:

Variant related genes	Relation type
ENSG00000143947	Chromatin interaction
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10172326	0.92[CEU][hapmap];0.87[CHB][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10193022	0.81[AFR][1000 genomes]
rs10197309	0.90[AMR][1000 genomes]
rs1133181	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1133182	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11679663	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11685292	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12616435	0.83[ASN][1000 genomes]
rs12619400	0.80[ASN][1000 genomes]
rs12621144	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13012766	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13013134	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13019355	0.88[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13021215	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13023235	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13417057	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs14026	0.94[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1437391	0.83[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.89[YRI][hapmap]
rs2164714	0.86[CEU][hapmap];0.85[ASN][1000 genomes]
rs2576710	0.82[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs2576724	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2864818	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34054131	0.85[ASN][1000 genomes]
rs34564471	0.88[ASN][1000 genomes]
rs35026006	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35161040	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35890669	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762509	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3935223	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671241	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671242	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4672024	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4672026	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4672027	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56095114	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs56339196	0.83[ASN][1000 genomes]
rs6545474	0.92[CEU][hapmap];0.87[CHB][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6545475	0.86[CHB][hapmap];0.95[CHD][hapmap];0.82[ASN][1000 genomes]
rs6545478	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6714830	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6759911	0.83[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7595134	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4420737	C2orf63	cis	cerebellum	SCAN
rs4420737	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55395600-55422800	Weak transcription	Ovary	ovary
2	chr2:55395600-55427000	Weak transcription	Left Ventricle	heart
3	chr2:55395800-55427000	Weak transcription	Aorta	Aorta
4	chr2:55397200-55450000	Weak transcription	NH-A	brain
5	chr2:55397400-55422400	Weak transcription	HSMMtube	muscle
6	chr2:55397400-55423000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:55399600-55423000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:55402600-55423200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:55402800-55450000	Weak transcription	NHDF-Ad	bronchial
10	chr2:55403200-55423800	Weak transcription	Osteobl	bone
11	chr2:55403200-55426800	Weak transcription	Colon Smooth Muscle	Colon
12	chr2:55403200-55431800	Weak transcription	Fetal Brain Male	brain
13	chr2:55403400-55423000	Weak transcription	NHEK	skin
14	chr2:55404200-55423000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:55405400-55423000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr2:55406800-55423000	Weak transcription	Lung	lung
17	chr2:55408600-55423000	Weak transcription	Pancreas	Pancrea
18	chr2:55408800-55423600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr2:55409000-55423000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:55409200-55425800	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr2:55410000-55424000	Weak transcription	Fetal Thymus	thymus
22	chr2:55410600-55422800	Weak transcription	HepG2	liver
23	chr2:55411200-55427000	Weak transcription	Primary B cells from cord blood	blood
24	chr2:55412200-55423000	Weak transcription	Dnd41	blood
25	chr2:55412600-55423000	Weak transcription	Thymus	Thymus
26	chr2:55412800-55428200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:55413000-55427000	Weak transcription	Brain Angular Gyrus	brain
28	chr2:55413600-55427000	Weak transcription	Fetal Lung	lung
29	chr2:55414600-55427000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:55414800-55423200	Weak transcription	Spleen	Spleen
31	chr2:55415400-55450000	Weak transcription	GM12878-XiMat	blood
32	chr2:55415600-55423000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:55416000-55426800	Weak transcription	Fetal Kidney	kidney
34	chr2:55416000-55428400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr2:55416200-55428800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:55416800-55423000	Weak transcription	Esophagus	oesophagus
37	chr2:55416800-55450000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr2:55417200-55422800	Weak transcription	Primary T cells from cord blood	blood
39	chr2:55417400-55423600	Weak transcription	Brain Germinal Matrix	brain
40	chr2:55417400-55450200	Weak transcription	Placenta	Placenta
41	chr2:55417800-55439200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:55417800-55450000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:55418000-55423200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:55418400-55433600	Weak transcription	Brain Anterior Caudate	brain
45	chr2:55419200-55423000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:55419200-55427000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr2:55419200-55429600	Weak transcription	Fetal Intestine Large	intestine
48	chr2:55419400-55422200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:55419400-55423000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:55419400-55434400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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