Variant report

Variant	rs3771222
Chromosome Location	chr2:58456277-58456278
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	chr2:58454709..58457250-chr2:58468268..58470995,2	K562	blood:
2	chr2:58455073..58459456-chr2:58466641..58469255,4	K562	blood:

Variant related genes	Relation type
ENSG00000273063	Chromatin interaction
ENSG00000115392	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10167028	0.91[CEU][hapmap]
rs10184957	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs10198382	0.83[CEU][hapmap];0.94[GIH][hapmap]
rs10203887	0.91[CEU][hapmap]
rs11903212	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12616896	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12624152	1.00[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12713376	0.94[EUR][1000 genomes]
rs12713378	0.94[JPT][hapmap]
rs12988249	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13001078	0.91[CEU][hapmap]
rs13006005	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13023405	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13032851	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13033987	0.91[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap]
rs13384786	0.91[CEU][hapmap];0.94[GIH][hapmap]
rs13386998	0.83[CEU][hapmap]
rs13410228	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13422760	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13424099	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap]
rs1404457	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1404459	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1404460	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17183100	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs34335951	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34556232	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35341336	1.00[AFR][1000 genomes]
rs35773188	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35925771	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3755296	0.88[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3771220	0.83[CEU][hapmap]
rs55809167	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57267169	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61746304	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6709533	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6714952	0.83[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6752935	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7558066	1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7561771	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9973679	0.94[JPT][hapmap]
rs9973912	0.82[CHD][hapmap];0.94[JPT][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	nsv999042	chr2:58326123-58530903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv535734	chr2:58326123-58530903	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1007527	chr2:58386271-58477536	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv535735	chr2:58386271-58477536	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58391000-58467000	Weak transcription	HMEC	breast
2	chr2:58414000-58461400	Weak transcription	NHEK	skin
3	chr2:58416600-58467200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:58432000-58466400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr2:58437000-58460200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:58437200-58459000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:58437800-58456800	Weak transcription	Fetal Kidney	kidney
8	chr2:58438600-58466400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:58439000-58467400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:58439200-58457000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:58439200-58457600	Weak transcription	Placenta	Placenta
12	chr2:58440000-58465000	Weak transcription	Fetal Brain Male	brain
13	chr2:58440000-58467400	Weak transcription	Primary B cells from peripheral blood	blood
14	chr2:58440600-58462000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:58440600-58467400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:58440800-58457600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:58441000-58458200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:58443400-58460400	Weak transcription	Brain Germinal Matrix	brain
19	chr2:58443600-58462200	Weak transcription	Brain Substantia Nigra	brain
20	chr2:58444200-58466200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:58448800-58464800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:58449400-58462400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:58450000-58466200	Weak transcription	HUVEC	blood vessel
24	chr2:58451000-58458000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr2:58451200-58457400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:58451400-58457000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:58451400-58457200	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr2:58451800-58457000	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:58452000-58457000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:58452000-58467400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr2:58452000-58467400	Weak transcription	NHLF	lung
32	chr2:58452200-58459000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr2:58452400-58457200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:58452600-58460600	Weak transcription	Brain Hippocampus Middle	brain
35	chr2:58453000-58456800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:58453200-58456400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:58453200-58457000	Strong transcription	A549	lung
38	chr2:58453200-58458400	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:58453800-58467400	Weak transcription	NHDF-Ad	bronchial
40	chr2:58454200-58456600	Strong transcription	Dnd41	blood
41	chr2:58454600-58457800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:58454600-58466800	Weak transcription	HSMM	muscle
43	chr2:58454800-58457200	Enhancers	Liver	Liver
44	chr2:58454800-58457600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr2:58454800-58457600	Weak transcription	Right Ventricle	heart
46	chr2:58454800-58458000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr2:58454800-58458600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:58454800-58460600	Weak transcription	Small Intestine	intestine
49	chr2:58454800-58462000	Weak transcription	K562	blood
50	chr2:58454800-58464400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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