Variant report

Variant	rs2272515
Chromosome Location	chr3:120134883-120134884
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:120066683..120069850-chr3:120134285..120137656,5	MCF-7	breast:
2	chr3:120066496..120069971-chr3:120134010..120137845,6	MCF-7	breast:
3	chr3:120133952..120135964-chr3:121186805..121189623,2	MCF-7	breast:
4	chr3:119961477..119964195-chr3:120134350..120136316,3	MCF-7	breast:
5	chr3:120048937..120051112-chr3:120133444..120135223,2	K562	blood:

Variant related genes	Relation type
ENSG00000240661	Chromatin interaction
ENSG00000163428	Chromatin interaction
ENSG00000175697	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1056928	1.00[JPT][hapmap]
rs1147696	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1147698	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1147699	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12173	0.87[EUR][1000 genomes]
rs12192	0.87[EUR][1000 genomes]
rs1259293	0.90[LWK][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes]
rs1259294	0.87[YRI][hapmap]
rs1259328	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13061630	1.00[JPT][hapmap]
rs13081675	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs13081694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13088020	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13096256	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs13096973	0.88[EUR][1000 genomes]
rs13097755	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13100865	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs13709	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1492272	1.00[JPT][hapmap]
rs1515577	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17813772	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs1879434	0.83[AFR][1000 genomes]
rs1969356	1.00[JPT][hapmap]
rs2030414	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2091726	0.96[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs2488	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs33935225	0.87[EUR][1000 genomes]
rs34446218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34805176	0.86[EUR][1000 genomes]
rs36001904	0.81[EUR][1000 genomes]
rs36068602	0.90[EUR][1000 genomes]
rs3755558	0.87[EUR][1000 genomes]
rs4146299	1.00[JPT][hapmap]
rs4146300	1.00[JPT][hapmap]
rs4676698	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs4676776	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs4676778	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4676779	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4676781	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs4676782	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs4676783	0.96[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs56100867	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438575	1.00[JPT][hapmap]
rs6775963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs869247	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs939500	0.87[YRI][hapmap]
rs9880550	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	esv3333135	chr3:120131862-120135010	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2272515	CD80	cis	cerebellum	SCAN
rs2272515	C3orf1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120114400-120143200	Weak transcription	Small Intestine	intestine
2	chr3:120115800-120151000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:120118800-120135600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:120122200-120136000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:120122400-120135000	Weak transcription	Psoas Muscle	Psoas
6	chr3:120122400-120135800	Weak transcription	A549	lung
7	chr3:120127400-120135600	Weak transcription	Fetal Thymus	thymus
8	chr3:120128200-120135000	Weak transcription	Thymus	Thymus
9	chr3:120128200-120137600	Weak transcription	Gastric	stomach
10	chr3:120128400-120135600	Weak transcription	Brain Germinal Matrix	brain
11	chr3:120128400-120135600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:120128400-120136200	Weak transcription	Fetal Brain Female	brain
13	chr3:120128600-120135600	Weak transcription	Esophagus	oesophagus
14	chr3:120128600-120135600	Weak transcription	Pancreas	Pancrea
15	chr3:120128600-120135600	Weak transcription	Spleen	Spleen
16	chr3:120128800-120135000	Weak transcription	Brain Angular Gyrus	brain
17	chr3:120128800-120135800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:120129800-120135600	Weak transcription	HMEC	breast
19	chr3:120130600-120135800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:120130800-120135400	Weak transcription	Brain Substantia Nigra	brain
21	chr3:120131000-120135600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:120131000-120135600	Weak transcription	Colonic Mucosa	Colon
23	chr3:120131200-120135600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:120131200-120135600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:120131200-120135800	Weak transcription	Ovary	ovary
26	chr3:120131200-120136000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr3:120131400-120135400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:120131400-120135600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:120131400-120135600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:120131600-120135600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:120132000-120135200	Weak transcription	Fetal Heart	heart
32	chr3:120132400-120135200	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:120132400-120135400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:120132400-120135400	Weak transcription	Liver	Liver
35	chr3:120132400-120135600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:120132400-120135600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:120132400-120135600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr3:120132400-120135600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr3:120132400-120135600	Weak transcription	Fetal Intestine Small	intestine
40	chr3:120132400-120135800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr3:120132400-120135800	Weak transcription	Stomach Mucosa	stomach
42	chr3:120132400-120135800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr3:120132400-120136600	Weak transcription	Aorta	Aorta
44	chr3:120132600-120135000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:120132600-120135000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr3:120132600-120135000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr3:120132600-120135200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:120132600-120135200	Weak transcription	Brain Anterior Caudate	brain
49	chr3:120132600-120135600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:120132600-120135600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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