Variant report

Variant	rs2688600
Chromosome Location	chr3:136252596-136252597
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1017882	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1070228	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10804640	0.85[EUR][1000 genomes]
rs10935183	0.84[EUR][1000 genomes]
rs10935185	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10935186	0.87[AMR][1000 genomes]
rs11719310	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11919030	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12163529	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12492510	0.84[EUR][1000 genomes]
rs2688601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34438032	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4038587	0.82[AMR][1000 genomes]
rs4521165	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4630889	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4678269	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4678436	0.84[AMR][1000 genomes]
rs55970317	0.85[AMR][1000 genomes]
rs6439649	0.84[AMR][1000 genomes]
rs6791142	0.84[AMR][1000 genomes]
rs6808312	0.85[AMR][1000 genomes]
rs711975	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs711977	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73226190	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73228043	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7427564	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7432375	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7618518	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7621308	0.83[ASN][1000 genomes]
rs833861	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs940174	0.85[AMR][1000 genomes]
rs9714347	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
6	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
7	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
8	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
9	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
10	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
11	nsv877528	chr3:136209550-136295283	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv591850	chr3:136209550-136300732	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	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
14	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
rs2688600	PCCB	cis	multi-tissue	Pritchard
rs2688600	PCCB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136176400-136314200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:136176600-136260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:136176800-136266200	Weak transcription	Hela-S3	cervix
4	chr3:136191400-136268000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:136195400-136278800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:136212200-136323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:136213000-136326600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:136220600-136266200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:136222400-136266200	Weak transcription	HSMM	muscle
10	chr3:136232000-136263600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:136232400-136255200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:136246600-136286200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:136247200-136319800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:136247200-136334800	Weak transcription	Aorta	Aorta
15	chr3:136247400-136270600	Weak transcription	Fetal Thymus	thymus
16	chr3:136247800-136255200	Weak transcription	Fetal Stomach	stomach
17	chr3:136247800-136261600	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr3:136248200-136349200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:136249800-136254200	Weak transcription	Lung	lung
20	chr3:136250000-136257000	Weak transcription	Fetal Intestine Small	intestine
21	chr3:136250800-136252600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:136251000-136252800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
23	chr3:136251000-136252800	ZNF genes & repeats	Dnd41	blood
24	chr3:136251000-136254400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:136251200-136252600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:136251200-136252800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
27	chr3:136251200-136253200	ZNF genes & repeats	Fetal Muscle Leg	muscle
28	chr3:136251400-136319000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:136251600-136252800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr3:136251600-136253000	Strong transcription	Primary B cells from cord blood	blood
31	chr3:136251600-136264400	Weak transcription	Fetal Lung	lung
32	chr3:136251600-136266000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr3:136251600-136270400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:136251600-136284400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:136251600-136284400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:136251600-136289400	Weak transcription	Adipose Nuclei	Adipose
37	chr3:136251600-136322400	Weak transcription	Liver	Liver
38	chr3:136251800-136252600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr3:136251800-136257400	Weak transcription	Fetal Intestine Large	intestine
40	chr3:136251800-136262200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:136251800-136266400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr3:136251800-136284800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:136252000-136252600	Weak transcription	Esophagus	oesophagus
44	chr3:136252000-136270000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:136252200-136252600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:136252200-136252600	ZNF genes & repeats	Left Ventricle	heart
47	chr3:136252200-136252800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
48	chr3:136252200-136254600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:136252400-136252600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:136252400-136252600	ZNF genes & repeats	Thymus	Thymus

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