Variant report

Variant	rs12620037
Chromosome Location	chr2:128265139-128265140
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:128261114..128269570-chr2:128281581..128286258,13	K562	blood:
2	chr2:128262614..128267545-chr2:128280339..128284643,6	K562	blood:
3	chr2:128255754..128258823-chr2:128264549..128267686,3	K562	blood:
4	chr2:128263369..128266760-chr2:128270837..128273303,3	K562	blood:
5	chr2:128262034..128264615-chr2:128264870..128267413,2	K562	blood:
6	chr2:128264079..128266201-chr2:128268340..128270505,2	MCF-7	breast:
7	chr2:128252742..128255070-chr2:128263163..128265839,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163166	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10496663	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10928769	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11679431	0.93[CEU][hapmap]
rs11681225	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11682864	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11685630	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11688201	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11690086	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11892245	0.93[CHB][hapmap];0.81[ASN][1000 genomes]
rs12053309	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12233101	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12616100	0.82[ASN][1000 genomes]
rs12616200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12618494	0.93[CEU][hapmap];0.93[CHB][hapmap];0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12619773	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17015274	0.95[AFR][1000 genomes]
rs17015334	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015401	0.83[ASN][1000 genomes]
rs1864553	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2082182	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2099209	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2288655	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35208523	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3732205	0.81[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3889307	0.93[CEU][hapmap];0.93[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55688542	0.81[EUR][1000 genomes]
rs56100618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56261855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56327685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62156572	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62156576	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62156599	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6758364	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs72843327	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7586672	1.00[CEU][hapmap];0.93[CHB][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs777556	0.86[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs873099	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875014	chr2:128178415-128328375	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12620037	AC068282.3	cis	Thyroid	GTEx
rs12620037	AC068282.3	cis	Artery Tibial	GTEx
rs12620037	AC068282.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12620037	AC068282.3	cis	Muscle Skeletal	GTEx
rs12620037	AC068282.3	cis	Esophagus Mucosa	GTEx
rs12620037	AC068282.3	cis	lung	GTEx
rs12620037	AC068282.3	cis	Adipose Subcutaneous	GTEx
rs12620037	AC068282.3	cis	Nerve Tibial	GTEx
rs12620037	AC068282.3	cis	Esophagus Muscularis	GTEx
rs12620037	AC068282.3	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128223600-128268800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:128235200-128270000	Strong transcription	Dnd41	blood
3	chr2:128239400-128266200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:128239400-128266400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:128240600-128265600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:128246200-128271800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:128257600-128265800	Weak transcription	Psoas Muscle	Psoas
8	chr2:128262600-128265600	Weak transcription	Fetal Brain Female	brain
9	chr2:128262600-128266000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:128262600-128283000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:128263000-128265600	Weak transcription	Small Intestine	intestine
12	chr2:128263000-128265800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:128263000-128265800	Weak transcription	Fetal Brain Male	brain
14	chr2:128263000-128266200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr2:128263000-128267600	Weak transcription	Stomach Mucosa	stomach
16	chr2:128263000-128272000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:128263000-128281200	Weak transcription	Fetal Kidney	kidney
18	chr2:128263200-128265200	Weak transcription	HMEC	breast
19	chr2:128263200-128265200	Weak transcription	HUVEC	blood vessel
20	chr2:128263200-128265400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:128263200-128265600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:128263200-128265600	Weak transcription	Adipose Nuclei	Adipose
23	chr2:128263200-128265600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr2:128263200-128265600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:128263200-128265600	Weak transcription	Left Ventricle	heart
26	chr2:128263200-128265600	Weak transcription	Right Ventricle	heart
27	chr2:128263200-128265800	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:128263200-128265800	Weak transcription	Gastric	stomach
29	chr2:128263200-128265800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr2:128263200-128266200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr2:128263200-128266200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr2:128263200-128266400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:128263200-128267000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:128263200-128267400	Weak transcription	Primary B cells from cord blood	blood
35	chr2:128263200-128268600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:128263200-128268600	Weak transcription	Thymus	Thymus
37	chr2:128263200-128268800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr2:128263200-128269400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr2:128263200-128271400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:128263200-128271400	Weak transcription	Colonic Mucosa	Colon
41	chr2:128263200-128271600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:128263200-128271600	Weak transcription	Pancreas	Pancrea
43	chr2:128263200-128271600	Weak transcription	Spleen	Spleen
44	chr2:128263200-128271800	Weak transcription	Aorta	Aorta
45	chr2:128263200-128271800	Weak transcription	Brain Germinal Matrix	brain
46	chr2:128263200-128271800	Weak transcription	Esophagus	oesophagus
47	chr2:128263200-128282800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:128263400-128265600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr2:128263400-128265600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:128263400-128265600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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