Variant report

Variant	rs11719310
Chromosome Location	chr3:136196754-136196755
allele	C/T
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	POLR2A	chr3:136196702-136196792	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
STAG1	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1070228	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10804640	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10935183	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10935184	0.83[AMR][1000 genomes]
rs10935185	0.81[AMR][1000 genomes]
rs11717954	0.83[EUR][1000 genomes]
rs12492510	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1394094	0.88[ASN][1000 genomes]
rs2688600	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2688601	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4630889	0.82[AMR][1000 genomes]
rs4678269	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs655748	0.85[EUR][1000 genomes]
rs66691851	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6791611	0.80[AMR][1000 genomes]
rs696518	0.84[EUR][1000 genomes]
rs711975	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs711977	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73226190	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7427564	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs833861	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs834304	0.83[EUR][1000 genomes]
rs834305	0.84[EUR][1000 genomes]
rs864437	0.81[EUR][1000 genomes]
rs866758	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9714347	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv877524	chr3:136112109-136295283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv877525	chr3:136112109-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv877526	chr3:136149139-136310985	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv877527	chr3:136182053-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11719310	PCCB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136176400-136314200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:136176600-136212000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:136176600-136222800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:136176600-136224200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr3:136176600-136224400	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:136176600-136231800	Weak transcription	Psoas Muscle	Psoas
7	chr3:136176600-136240000	Weak transcription	HMEC	breast
8	chr3:136176600-136260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:136176800-136205800	Weak transcription	Small Intestine	intestine
10	chr3:136176800-136228000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:136176800-136266200	Weak transcription	Hela-S3	cervix
12	chr3:136177200-136236400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:136177400-136198400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr3:136178000-136212000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:136178400-136208200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:136178600-136220200	Weak transcription	Fetal Brain Male	brain
17	chr3:136179400-136204000	Weak transcription	Fetal Intestine Small	intestine
18	chr3:136179800-136212000	Weak transcription	Fetal Heart	heart
19	chr3:136181200-136205400	Weak transcription	Fetal Kidney	kidney
20	chr3:136181400-136211600	Weak transcription	A549	lung
21	chr3:136182000-136204400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:136183800-136212000	Weak transcription	Lung	lung
23	chr3:136189800-136197200	Strong transcription	Dnd41	blood
24	chr3:136189800-136197600	Weak transcription	Brain Substantia Nigra	brain
25	chr3:136191000-136220000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr3:136191400-136209400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:136191400-136268000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr3:136192000-136204000	Weak transcription	Fetal Stomach	stomach
29	chr3:136192200-136196800	Weak transcription	GM12878-XiMat	blood
30	chr3:136192200-136205400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:136192200-136212600	Weak transcription	Pancreas	Pancrea
32	chr3:136192200-136225600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:136192400-136196800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:136192400-136252400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr3:136192600-136206000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:136193800-136204800	Weak transcription	Fetal Brain Female	brain
37	chr3:136193800-136217200	Weak transcription	HepG2	liver
38	chr3:136193800-136231400	Weak transcription	NHLF	lung
39	chr3:136193800-136239200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:136194600-136212000	Weak transcription	Esophagus	oesophagus
41	chr3:136194800-136204000	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr3:136194800-136204400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr3:136195000-136210600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:136195000-136220400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:136195000-136223000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:136195200-136196800	Weak transcription	Brain Anterior Caudate	brain
47	chr3:136195200-136196800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:136195200-136197000	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr3:136195200-136205000	Weak transcription	Brain Germinal Matrix	brain
50	chr3:136195200-136209800	Weak transcription	NHDF-Ad	bronchial

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