Variant report

Variant	rs55970317
Chromosome Location	chr3:136353193-136353194
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	chr3:136350170..136353597-chr3:136468835..136472616,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118007	Chromatin interaction
ENSG00000261758	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1017882	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10935185	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10935186	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11919030	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12163529	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2688600	0.85[AMR][1000 genomes]
rs2688601	0.85[AMR][1000 genomes]
rs34438032	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4038587	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4408829	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4521165	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4630889	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4678436	0.90[AMR][1000 genomes]
rs6439649	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6791142	0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6808312	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs711975	0.81[EUR][1000 genomes]
rs73228043	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7427564	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7432375	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7618518	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7618871	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7637129	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs940174	0.96[AMR][1000 genomes];0.94[EUR][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	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55970317	PCCB	cis	multi-tissue	Pritchard
rs55970317	PCCB	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136308000-136357400	Weak transcription	Lung	lung
2	chr3:136315400-136356400	Weak transcription	Brain Anterior Caudate	brain
3	chr3:136315800-136355600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:136315800-136361000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr3:136316000-136364400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:136320800-136356800	Weak transcription	Ovary	ovary
7	chr3:136322200-136355200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:136323400-136362000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:136324200-136363600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:136327400-136357400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:136335600-136357400	Weak transcription	Psoas Muscle	Psoas
12	chr3:136336200-136364800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:136338800-136355600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:136342200-136355600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:136344600-136355600	Weak transcription	Fetal Kidney	kidney
16	chr3:136345800-136364000	Weak transcription	Small Intestine	intestine
17	chr3:136347000-136361200	Weak transcription	Left Ventricle	heart
18	chr3:136347200-136368400	Weak transcription	Fetal Intestine Small	intestine
19	chr3:136347400-136358400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:136347400-136364000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:136347600-136353400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:136347600-136367200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:136348200-136353800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:136348200-136365000	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr3:136348600-136364600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:136348800-136363800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr3:136348800-136373600	Weak transcription	Thymus	Thymus
28	chr3:136349800-136357400	Weak transcription	Fetal Thymus	thymus
29	chr3:136349800-136372400	Weak transcription	Dnd41	blood
30	chr3:136350400-136353200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:136350600-136372200	Weak transcription	Primary T cells from cord blood	blood
32	chr3:136351400-136355600	Weak transcription	Aorta	Aorta
33	chr3:136351600-136354200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr3:136351600-136355600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr3:136351600-136364600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr3:136351600-136364800	Weak transcription	Pancreas	Pancrea
37	chr3:136351600-136376200	Weak transcription	Esophagus	oesophagus
38	chr3:136351800-136355600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:136351800-136364000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:136351800-136364600	Weak transcription	Right Ventricle	heart
41	chr3:136352000-136364000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:136352200-136355600	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:136352400-136355400	Weak transcription	NH-A	brain
44	chr3:136352400-136355600	Weak transcription	Liver	Liver
45	chr3:136352400-136357800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr3:136352400-136361600	Weak transcription	Right Atrium	heart
47	chr3:136352400-136371600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:136352400-136371600	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:136352400-136371800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:136352800-136356200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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