Variant report

Variant	rs655748
Chromosome Location	chr3:136103287-136103288
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135954886..135956782-chr3:136102988..136105563,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10804640	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10935181	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10935182	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10935183	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10935184	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11717954	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11719310	0.85[EUR][1000 genomes]
rs11915629	0.80[AMR][1000 genomes]
rs12492510	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4678269	0.83[EUR][1000 genomes]
rs517319	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs521746	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56235965	0.84[AMR][1000 genomes]
rs619605	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs655836	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs66691851	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6791611	0.81[AMR][1000 genomes]
rs696518	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs698269	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs711972	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73222302	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73226190	0.84[EUR][1000 genomes]
rs834304	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs834305	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs864437	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs866758	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9714347	0.84[EUR][1000 genomes]

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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv877520	chr3:136056861-136310985	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv877521	chr3:136069286-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv877522	chr3:136088038-136241028	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv877523	chr3:136088038-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv520012	chr3:136088038-136314119	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv238089	chr3:136098002-136105895	Weak transcription Strong transcription ZNF genes & repeats Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs655748	PCCB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136054600-136172000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:136063400-136139000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr3:136063400-136139000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:136063600-136105600	Weak transcription	Gastric	stomach
5	chr3:136063600-136110600	Weak transcription	Small Intestine	intestine
6	chr3:136063600-136139200	Weak transcription	Pancreas	Pancrea
7	chr3:136067600-136109000	Weak transcription	HUVEC	blood vessel
8	chr3:136068600-136103800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr3:136069400-136121200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:136069600-136107400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:136069600-136138800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:136069600-136139400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:136069800-136106600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:136069800-136118800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:136069800-136159600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:136070600-136105800	Weak transcription	Psoas Muscle	Psoas
17	chr3:136070800-136112200	Weak transcription	Aorta	Aorta
18	chr3:136070800-136121400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:136075000-136137800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:136075400-136108000	Weak transcription	Fetal Brain Female	brain
21	chr3:136075600-136105800	Weak transcription	Ovary	ovary
22	chr3:136075800-136160200	Weak transcription	Brain Germinal Matrix	brain
23	chr3:136079400-136174200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:136081200-136118800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:136083200-136111400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:136084400-136123200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:136085400-136104200	Weak transcription	GM12878-XiMat	blood
28	chr3:136085600-136116400	Weak transcription	Fetal Intestine Large	intestine
29	chr3:136085800-136116400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:136085800-136139200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr3:136085800-136174800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:136086000-136112200	Weak transcription	Liver	Liver
33	chr3:136086000-136128400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr3:136086000-136136000	Weak transcription	HSMM	muscle
35	chr3:136086200-136174800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr3:136086400-136116800	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr3:136088200-136106400	Weak transcription	Primary B cells from peripheral blood	blood
38	chr3:136088400-136121200	Weak transcription	Thymus	Thymus
39	chr3:136092200-136108000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr3:136093200-136117000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:136094600-136115800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:136095600-136103800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:136095600-136104600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:136095600-136116200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr3:136095600-136117200	Weak transcription	Placenta	Placenta
46	chr3:136095600-136121000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:136095600-136132400	Weak transcription	Left Ventricle	heart
48	chr3:136095600-136132600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr3:136095600-136134400	Weak transcription	Adipose Nuclei	Adipose
50	chr3:136095600-136137800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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