Variant report

Variant	rs12486911
Chromosome Location	chr3:136558953-136558954
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr3:136558892-136559517	SK-N-SH	brain:	n/a	chr3:136559109-136559118
2	ZNF384	chr3:136557466-136559394	K562	blood:	n/a	n/a
3	RCOR1	chr3:136558543-136559443	K562	blood:	n/a	n/a
4	TBL1XR1	chr3:136558949-136559396	K562	blood:	n/a	n/a
5	POLR2A	chr3:136558933-136558961	K562	blood:	n/a	n/a
6	JUN	chr3:136558821-136559533	K562	blood:	n/a	n/a
7	JUND	chr3:136558723-136559451	K562	blood:	n/a	n/a
8	JUN	chr3:136558868-136559418	K562	blood:	n/a	n/a
9	POLR2A	chr3:136557766-136559493	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136471409..136475684-chr3:136558625..136561500,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273486	TF binding region
ENSG00000261758	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10935199	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12054219	0.84[CEU][hapmap]
rs12054408	0.80[CEU][hapmap]
rs1609391	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1681817	1.00[YRI][hapmap]
rs1729951	1.00[YRI][hapmap]
rs17366234	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2062322	1.00[YRI][hapmap]
rs28458819	0.83[EUR][1000 genomes]
rs28877307	0.81[EUR][1000 genomes]
rs34799319	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4408829	1.00[YRI][hapmap]
rs4420814	0.82[EUR][1000 genomes]
rs4521165	1.00[YRI][hapmap]
rs4678441	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs4678442	0.86[EUR][1000 genomes]
rs56163507	0.81[EUR][1000 genomes]
rs56695781	0.82[EUR][1000 genomes]
rs60574021	0.83[EUR][1000 genomes]
rs6439649	1.00[YRI][hapmap]
rs6439655	1.00[YRI][hapmap]
rs67782618	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6791142	1.00[YRI][hapmap]
rs6793936	0.81[EUR][1000 genomes]
rs6802291	0.84[EUR][1000 genomes]
rs6802702	1.00[YRI][hapmap]
rs7616204	1.00[YRI][hapmap]
rs7618518	1.00[YRI][hapmap]
rs7618871	1.00[YRI][hapmap]
rs7621932	0.82[EUR][1000 genomes]
rs7633629	0.82[EUR][1000 genomes]
rs835632	0.84[CEU][hapmap]
rs835634	0.84[CEU][hapmap]
rs835637	0.92[CEU][hapmap]
rs835649	0.92[CEU][hapmap]
rs900818	1.00[YRI][hapmap]
rs9757179	0.84[EUR][1000 genomes]
rs9836231	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877530	chr3:136514310-136604697	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	n/a
2	nsv877531	chr3:136517016-136662954	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv877532	chr3:136526939-136662603	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv877533	chr3:136539689-136662954	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12486911	PCCB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136550800-136561000	Weak transcription	Thymus	Thymus
2	chr3:136551600-136574000	Weak transcription	HepG2	liver
3	chr3:136552400-136570800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr3:136552600-136579400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:136553400-136560200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:136554200-136561000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:136554600-136559400	Enhancers	Fetal Brain Male	brain
8	chr3:136554800-136578400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:136554800-136579400	Weak transcription	Fetal Lung	lung
10	chr3:136555000-136574000	Weak transcription	Ovary	ovary
11	chr3:136555200-136559200	Enhancers	Fetal Brain Female	brain
12	chr3:136555200-136561600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:136555200-136564600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:136555400-136561200	Weak transcription	Fetal Intestine Small	intestine
15	chr3:136555400-136561200	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:136555400-136579200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr3:136555600-136577800	Weak transcription	Lung	lung
18	chr3:136555600-136579200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr3:136555600-136580000	Weak transcription	Esophagus	oesophagus
20	chr3:136555800-136559000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:136556000-136573400	Weak transcription	GM12878-XiMat	blood
22	chr3:136556400-136559400	Enhancers	Primary hematopoietic stem cells	blood
23	chr3:136557200-136559200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr3:136557200-136559400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:136557200-136559400	Enhancers	NH-A	brain
26	chr3:136557200-136559400	Enhancers	Osteobl	bone
27	chr3:136557200-136563200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:136557400-136559000	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr3:136557400-136559000	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr3:136557400-136559000	Enhancers	Colon Smooth Muscle	Colon
31	chr3:136557400-136559000	Enhancers	Stomach Smooth Muscle	stomach
32	chr3:136557400-136559200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:136557400-136559200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:136557400-136559200	Enhancers	Adipose Nuclei	Adipose
35	chr3:136557400-136559200	Enhancers	Hela-S3	cervix
36	chr3:136557400-136559400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:136557400-136559400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:136557600-136559000	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr3:136557600-136559000	Enhancers	Brain Angular Gyrus	brain
40	chr3:136557600-136559000	Enhancers	Brain Anterior Caudate	brain
41	chr3:136557600-136559000	Enhancers	HSMMtube	muscle
42	chr3:136557600-136559400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:136557600-136559400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr3:136557600-136559400	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr3:136557600-136561200	Weak transcription	Fetal Stomach	stomach
46	chr3:136557800-136559200	Enhancers	NHLF	lung
47	chr3:136557800-136559800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:136558000-136559000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:136558000-136559000	Enhancers	Brain Hippocampus Middle	brain
50	chr3:136558000-136559400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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