Variant report

Variant	rs12478842
Chromosome Location	chr2:113550688-113550689
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113533014..113535192-chr2:113549510..113553376,4	K562	blood:
2	chr2:113402003..113404978-chr2:113549720..113551428,2	K562	blood:
3	chr2:113403478..113405250-chr2:113549720..113552295,2	K562	blood:

Variant related genes	Relation type
ENSG00000144136	Chromatin interaction
ENSG00000237753	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10165537	0.82[CHB][hapmap]
rs10167914	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10193063	0.82[CHB][hapmap]
rs10200192	0.82[CHB][hapmap]
rs10496444	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10496445	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11676014	0.93[ASN][1000 genomes]
rs11687624	0.96[ASN][1000 genomes]
rs12471565	0.91[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12612788	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12622683	0.81[CHB][hapmap]
rs12711741	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13000462	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13009294	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13013602	0.82[CHB][hapmap]
rs13015273	0.90[CHB][hapmap]
rs13016817	0.90[CHB][hapmap]
rs13019249	0.84[CHB][hapmap]
rs13026263	0.81[CHB][hapmap]
rs13027814	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533463	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1609682	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17649681	0.82[CHB][hapmap]
rs1969294	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071373	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071376	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3783512	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3783513	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3783516	0.81[CHB][hapmap]
rs3783521	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3783525	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3783526	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3783533	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3783539	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3783543	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3783546	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3783550	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3811040	0.81[CHB][hapmap]
rs4402765	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4848298	0.81[CHB][hapmap]
rs4848301	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4848302	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542095	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6706663	0.81[CHB][hapmap]
rs6712572	0.82[CHB][hapmap]
rs6721044	0.82[CHB][hapmap]
rs6746923	0.81[CHB][hapmap]
rs6753803	0.81[CHB][hapmap]
rs7369378	0.93[ASN][1000 genomes]
rs74182856	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7567619	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7577241	0.81[CHB][hapmap]
rs908551	0.81[CHB][hapmap]

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	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1010106	chr2:113394981-113556071	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113534000-113551800	Weak transcription	Fetal Heart	heart
2	chr2:113542400-113559200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:113543000-113562200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:113545600-113551000	Weak transcription	Adipose Nuclei	Adipose
5	chr2:113545800-113552400	Weak transcription	Primary B cells from cord blood	blood
6	chr2:113546600-113550800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:113546600-113551600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:113547800-113551800	Weak transcription	Right Atrium	heart
9	chr2:113548000-113554800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:113548200-113550800	Weak transcription	A549	lung
11	chr2:113548400-113553800	Enhancers	Placenta	Placenta
12	chr2:113548600-113554400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:113549200-113553800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr2:113549400-113550800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr2:113549400-113552000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:113549400-113552400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:113549400-113552400	Weak transcription	Esophagus	oesophagus
18	chr2:113549400-113553200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:113549400-113555200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr2:113549800-113551600	Enhancers	K562	blood
21	chr2:113549800-113553200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:113550000-113551400	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr2:113550000-113552000	Enhancers	HepG2	liver
24	chr2:113550000-113552600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:113550400-113554400	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr2:113550400-113554400	Enhancers	HMEC	breast
27	chr2:113550600-113551200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:113550600-113551200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr2:113550600-113551200	Flanking Active TSS	NHEK	skin
30	chr2:113550600-113552400	Enhancers	Hela-S3	cervix
31	chr2:113550600-113552800	Enhancers	HUVEC	blood vessel
32	chr2:113550600-113553800	Enhancers	Fetal Lung	lung
33	chr2:113550600-113554400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:113550600-113554400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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