Variant report

Variant	rs7557796
Chromosome Location	chr2:86766153-86766154
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86765939..86767905-chr2:86790325..86791926,2	MCF-7	breast:
2	chr2:86763873..86766735-chr2:86781527..86783307,2	K562	blood:
3	chr2:86759845..86761592-chr2:86766001..86768236,2	K562	blood:

Variant related genes	Relation type
ENSG00000115561	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1015117	0.88[CHB][hapmap];0.81[GIH][hapmap]
rs10184584	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10184879	0.88[CHB][hapmap]
rs10184985	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10187880	0.88[CHB][hapmap];0.81[ASN][1000 genomes]
rs10188515	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1036940	0.83[GIH][hapmap]
rs11127045	0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs11127046	0.83[ASN][1000 genomes]
rs11127047	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11676576	0.83[ASN][1000 genomes]
rs12613282	0.86[CHB][hapmap]
rs12614447	0.88[CHB][hapmap];0.81[GIH][hapmap]
rs12615285	0.88[CHB][hapmap];0.81[GIH][hapmap];0.83[ASN][1000 genomes]
rs12623509	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs12714188	0.83[ASN][1000 genomes]
rs12714190	0.96[CEU][hapmap];0.88[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.81[EUR][1000 genomes]
rs12714199	0.96[CEU][hapmap];0.88[CHB][hapmap]
rs12987172	0.88[CHB][hapmap];0.81[GIH][hapmap]
rs12995117	0.83[GIH][hapmap]
rs13015620	0.88[CHB][hapmap];0.81[GIH][hapmap]
rs13034615	0.88[CHB][hapmap];0.81[GIH][hapmap];0.83[ASN][1000 genomes]
rs13390713	0.83[ASN][1000 genomes]
rs13408041	0.82[ASN][1000 genomes]
rs13429696	0.83[ASN][1000 genomes]
rs1518807	0.88[CHB][hapmap]
rs1629293	0.88[CHB][hapmap]
rs2044230	0.83[GIH][hapmap]
rs218060	0.85[GIH][hapmap]
rs2241803	0.88[CHB][hapmap];0.81[GIH][hapmap]
rs2367546	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs308901	0.85[GIH][hapmap]
rs308907	0.91[GIH][hapmap]
rs308911	0.91[GIH][hapmap]
rs3201448	0.88[CHB][hapmap];0.81[GIH][hapmap]
rs3755002	0.88[CHB][hapmap];0.81[GIH][hapmap]
rs396354	0.85[GIH][hapmap]
rs4832040	0.82[ASN][1000 genomes]
rs4832043	0.91[ASN][1000 genomes]
rs4832290	0.83[GIH][hapmap]
rs4832294	0.83[GIH][hapmap]
rs4832296	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4832297	0.83[ASN][1000 genomes]
rs4832298	0.83[EUR][1000 genomes]
rs4832300	0.88[CHB][hapmap];0.81[GIH][hapmap]
rs6547700	0.80[GIH][hapmap]
rs6714826	0.83[GIH][hapmap]
rs6738663	0.88[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap]
rs6750226	0.88[CHB][hapmap];0.81[GIH][hapmap]
rs6752371	0.96[CEU][hapmap];0.88[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap]
rs683139	0.82[GIH][hapmap]
rs7568840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7584882	0.96[CEU][hapmap];0.88[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap]
rs7587034	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7593151	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7596717	0.96[CEU][hapmap];0.88[CHB][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8179729	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9284788	0.88[CHB][hapmap];0.81[GIH][hapmap];0.82[ASN][1000 genomes]

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	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7557796	PTCD3	cis	cerebellum	SCAN
rs7557796	VPS24	Cis_1M	lymphoblastoid	RTeQTL
rs7557796	VPS24	cis	multi-tissue	Pritchard
rs7557796	POLR1A	cis	cerebellum	SCAN
rs7557796	IMMT	cis	lymphoblastoid	seeQTL
rs7557796	VPS24	cis	lymphoblastoid	seeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86734000-86784800	Weak transcription	Osteobl	bone
2	chr2:86736400-86770600	Weak transcription	Brain Angular Gyrus	brain
3	chr2:86737000-86772800	Weak transcription	Pancreas	Pancrea
4	chr2:86737400-86788400	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:86737600-86768400	Weak transcription	Ovary	ovary
6	chr2:86737800-86779600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr2:86738200-86772400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:86738200-86772600	Weak transcription	Right Ventricle	heart
9	chr2:86741400-86768400	Weak transcription	Psoas Muscle	Psoas
10	chr2:86746000-86768000	Weak transcription	Fetal Heart	heart
11	chr2:86748000-86770600	Weak transcription	Gastric	stomach
12	chr2:86749400-86772600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:86749400-86775000	Weak transcription	NH-A	brain
14	chr2:86750000-86772400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:86750400-86773600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:86753800-86788400	Weak transcription	HSMM	muscle
17	chr2:86754000-86774000	Weak transcription	Hela-S3	cervix
18	chr2:86756000-86788400	Weak transcription	Brain Anterior Caudate	brain
19	chr2:86756400-86772600	Weak transcription	Lung	lung
20	chr2:86756400-86773800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr2:86756600-86766400	Weak transcription	Fetal Brain Male	brain
22	chr2:86756600-86770400	Weak transcription	Liver	Liver
23	chr2:86756600-86770400	Weak transcription	HepG2	liver
24	chr2:86756600-86771800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:86756600-86772400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:86756600-86772400	Weak transcription	Thymus	Thymus
27	chr2:86756600-86772600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:86756600-86773200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:86756600-86773600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr2:86756600-86776200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:86756600-86779000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:86756600-86779000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr2:86756600-86784800	Weak transcription	Left Ventricle	heart
34	chr2:86756600-86789200	Weak transcription	Aorta	Aorta
35	chr2:86756800-86772600	Weak transcription	Placenta	Placenta
36	chr2:86756800-86779400	Weak transcription	NHDF-Ad	bronchial
37	chr2:86757000-86773000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:86761200-86768000	Weak transcription	HSMMtube	muscle
39	chr2:86761200-86788600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:86761200-86788800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:86761400-86768200	Weak transcription	Adipose Nuclei	Adipose
42	chr2:86761400-86769000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:86761400-86779400	Weak transcription	NHEK	skin
44	chr2:86761600-86772600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr2:86761800-86772800	Weak transcription	Primary B cells from peripheral blood	blood
46	chr2:86761800-86773800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr2:86762800-86771800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr2:86763200-86771000	Weak transcription	A549	lung
49	chr2:86763800-86766800	Strong transcription	Primary B cells from cord blood	blood
50	chr2:86763800-86767600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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