Variant report

Variant	rs2249322
Chromosome Location	chr3:133554026-133554027
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:133551283..133554074-chr3:133613928..133616340,2	MCF-7	breast:
2	chr3:133551780..133554381-chr3:133557362..133559309,2	K562	blood:
3	chr3:133551846..133555419-chr3:133559086..133561018,3	K562	blood:

Variant related genes	Relation type
ENSG00000154917	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1043147	0.85[JPT][hapmap]
rs11710936	0.83[CEU][hapmap]
rs12487258	0.81[CEU][hapmap]
rs12637730	0.89[JPT][hapmap]
rs16840994	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs16841004	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs2293373	0.89[JPT][hapmap]
rs2293374	0.84[JPT][hapmap]
rs2692667	0.83[CEU][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2692668	1.00[CEU][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2692670	1.00[CEU][hapmap];1.00[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]
rs2692671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2692674	1.00[AFR][1000 genomes]
rs2715607	0.83[CEU][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2715608	0.83[CEU][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2715609	0.83[CEU][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2715636	0.81[CHB][hapmap];0.88[ASN][1000 genomes]
rs3811659	0.85[JPT][hapmap]
rs7626433	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877506	chr3:133423473-133569777	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv829729	chr3:133444871-133620387	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2249322	SRPRB	Cis_1M	lymphoblastoid	RTeQTL
rs2249322	SRPRB	cis	multi-tissue	Pritchard

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133539400-133572200	Weak transcription	Fetal Brain Male	brain
2	chr3:133541400-133558200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:133541400-133559600	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:133542000-133555400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:133542000-133563600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:133542600-133557800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:133542800-133569000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:133543400-133560600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:133543800-133560000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:133544000-133556600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:133544200-133557600	Weak transcription	Adipose Nuclei	Adipose
12	chr3:133544400-133559800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:133544600-133562200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:133544600-133573200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:133544600-133584200	Weak transcription	Esophagus	oesophagus
16	chr3:133545000-133582800	Weak transcription	Gastric	stomach
17	chr3:133545200-133557600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:133546200-133557400	Weak transcription	Fetal Intestine Small	intestine
19	chr3:133548000-133559600	Weak transcription	Lung	lung
20	chr3:133548000-133563400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:133548000-133564400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:133548200-133560600	Strong transcription	Brain Germinal Matrix	brain
23	chr3:133549000-133560000	Strong transcription	Brain Anterior Caudate	brain
24	chr3:133549200-133561200	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:133549200-133562400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:133549800-133560400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:133550000-133558200	Weak transcription	Fetal Heart	heart
28	chr3:133550000-133562200	Weak transcription	Right Atrium	heart
29	chr3:133550200-133560400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:133550400-133560200	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr3:133550400-133560800	Strong transcription	Fetal Brain Female	brain
32	chr3:133550600-133554200	Strong transcription	Brain Substantia Nigra	brain
33	chr3:133550800-133559200	Strong transcription	Fetal Muscle Trunk	muscle
34	chr3:133550800-133560000	Strong transcription	Brain Cingulate Gyrus	brain
35	chr3:133550800-133560400	Strong transcription	Stomach Smooth Muscle	stomach
36	chr3:133551000-133560000	Strong transcription	Brain Angular Gyrus	brain
37	chr3:133551600-133560200	Strong transcription	Fetal Stomach	stomach
38	chr3:133551800-133557200	Weak transcription	Aorta	Aorta
39	chr3:133552000-133558800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:133552400-133558200	Strong transcription	Spleen	Spleen
41	chr3:133552600-133558400	Strong transcription	Fetal Muscle Leg	muscle
42	chr3:133553200-133560400	Strong transcription	Right Ventricle	heart
43	chr3:133553400-133554600	Strong transcription	Pancreas	Pancrea
44	chr3:133553400-133555600	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:133553600-133557200	Weak transcription	Placenta	Placenta
46	chr3:133553800-133557800	Weak transcription	Left Ventricle	heart
47	chr3:133554000-133554400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:133554000-133554400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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