Variant report

Variant	rs570621
Chromosome Location	chr3:136000743-136000744
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135913736..135917229-chr3:135999064..136002214,3	K562	blood:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10935181	0.82[EUR][1000 genomes]
rs10935184	0.85[EUR][1000 genomes]
rs1153877	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488721	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1279086	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1279424	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1279949	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3957816	0.83[ASN][1000 genomes]
rs480162	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs480330	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs517319	0.80[AMR][1000 genomes]
rs518972	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs527888	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs553018	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs556788	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56235965	0.80[EUR][1000 genomes]
rs589092	0.96[ASN][1000 genomes]
rs590198	0.83[ASN][1000 genomes]
rs619605	0.82[AMR][1000 genomes]
rs632251	0.83[ASN][1000 genomes]
rs634559	0.83[ASN][1000 genomes]
rs650326	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs654237	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs655836	0.82[EUR][1000 genomes]
rs661739	0.83[ASN][1000 genomes]
rs664088	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66691851	0.81[EUR][1000 genomes]
rs668437	0.81[ASN][1000 genomes]
rs681783	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs684195	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs696081	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs696520	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs711972	0.80[EUR][1000 genomes]
rs73222302	0.81[EUR][1000 genomes]
rs838202	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs895894	0.83[ASN][1000 genomes]

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	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	nsv508246	chr3:135922023-136038622	Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs570621	PCCB	Cis_1M	lymphoblastoid	RTeQTL
rs570621	PCCB	cis	multi-tissue	Pritchard

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135970600-136039400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:135976200-136012400	Weak transcription	NHLF	lung
3	chr3:135976200-136016400	Weak transcription	Colonic Mucosa	Colon
4	chr3:135976200-136021600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:135981200-136052000	Weak transcription	NH-A	brain
6	chr3:135981600-136020400	Weak transcription	HUVEC	blood vessel
7	chr3:135982600-136004000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr3:135995000-136000800	ZNF genes & repeats	Fetal Brain Female	brain
9	chr3:135995000-136001200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:135995200-136001200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
11	chr3:135995200-136002200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:135995800-136001400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:135996800-136003600	Weak transcription	HMEC	breast
14	chr3:135996800-136016000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:135997000-136000800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr3:135997000-136001800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
17	chr3:135997000-136004000	Weak transcription	Right Ventricle	heart
18	chr3:135997000-136010600	Weak transcription	Gastric	stomach
19	chr3:135997000-136012000	Weak transcription	Spleen	Spleen
20	chr3:135997200-136002400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:135997400-136001000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:135997400-136002000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:135997400-136002600	Weak transcription	K562	blood
24	chr3:135997400-136015200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:135997600-136001000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:135997600-136001200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
27	chr3:135998000-136040200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:135998400-136002000	Weak transcription	Fetal Heart	heart
29	chr3:135998800-136001200	ZNF genes & repeats	Fetal Intestine Small	intestine
30	chr3:135999000-136000800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:135999000-136000800	ZNF genes & repeats	Brain Hippocampus Middle	brain
32	chr3:135999000-136000800	ZNF genes & repeats	Fetal Intestine Large	intestine
33	chr3:135999200-136001000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:135999200-136001000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:135999200-136001000	ZNF genes & repeats	Fetal Muscle Leg	muscle
36	chr3:135999600-136000800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr3:135999600-136001000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:135999600-136002800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr3:135999600-136004000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr3:135999600-136005400	Strong transcription	HepG2	liver
41	chr3:135999800-136000800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:135999800-136000800	Weak transcription	Primary T cells from cord blood	blood
43	chr3:135999800-136001400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:135999800-136001600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:135999800-136001800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:135999800-136002000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr3:135999800-136002000	Weak transcription	Fetal Stomach	stomach
48	chr3:135999800-136002000	Weak transcription	Ovary	ovary
49	chr3:135999800-136002000	Weak transcription	Pancreas	Pancrea
50	chr3:135999800-136002000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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