Variant report

Variant	rs11898288
Chromosome Location	chr2:173338045-173338046
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173331352..173333270-chr2:173337183..173340089,3	MCF-7	breast:
2	chr2:173330512..173332286-chr2:173336270..173339120,2	K562	blood:

Variant related genes	Relation type
ENSG00000232788	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10193201	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10460364	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13012170	0.85[JPT][hapmap]
rs1319059	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17664	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1920979	0.80[CEU][hapmap];0.83[TSI][hapmap]
rs2357634	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2357635	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2737086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3108778	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35968313	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4246629	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4972834	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4972835	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4972840	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5015856	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55978548	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62167825	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6433362	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710725	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6714597	0.80[CEU][hapmap]
rs6715425	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6723030	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6730905	0.85[EUR][1000 genomes]
rs6749369	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6759316	0.92[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs6759557	0.80[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs7570417	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7575064	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11898288	UBR3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173321400-173356000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:173326400-173340400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:173327200-173353200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:173327400-173338600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:173327400-173345000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:173327800-173370800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:173328800-173339000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:173328800-173353400	Weak transcription	Right Ventricle	heart
9	chr2:173329400-173344400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:173329800-173371200	Weak transcription	Hela-S3	cervix
11	chr2:173330200-173342200	Weak transcription	Brain Substantia Nigra	brain
12	chr2:173330200-173345600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:173330200-173350400	Weak transcription	Primary B cells from cord blood	blood
14	chr2:173330400-173339400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:173330400-173360400	Weak transcription	Small Intestine	intestine
16	chr2:173330600-173339000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr2:173330600-173339400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:173330600-173339600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:173330600-173344600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:173330600-173344800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:173330600-173344800	Weak transcription	Adipose Nuclei	Adipose
22	chr2:173330600-173345000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:173330600-173345000	Weak transcription	NH-A	brain
24	chr2:173330600-173345200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:173330600-173345600	Weak transcription	Brain Hippocampus Middle	brain
26	chr2:173330600-173346400	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr2:173330600-173351400	Weak transcription	Psoas Muscle	Psoas
28	chr2:173330600-173351400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr2:173330600-173351600	Weak transcription	Brain Anterior Caudate	brain
30	chr2:173330600-173352400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr2:173330600-173352600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr2:173330600-173352600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:173330600-173353200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr2:173330600-173353200	Weak transcription	Aorta	Aorta
35	chr2:173330600-173353400	Weak transcription	Fetal Stomach	stomach
36	chr2:173330600-173371400	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:173330600-173372200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr2:173330600-173373200	Strong transcription	NHEK	skin
39	chr2:173330600-173373400	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr2:173330600-173373400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:173330600-173373600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:173330600-173374200	Weak transcription	Stomach Mucosa	stomach
43	chr2:173330800-173345400	Weak transcription	NHLF	lung
44	chr2:173330800-173348200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:173331000-173341200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:173331000-173344800	Weak transcription	NHDF-Ad	bronchial
47	chr2:173331000-173346600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr2:173331000-173348400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr2:173331000-173370000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr2:173331000-173373200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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