Variant report

Variant	rs11915629
Chromosome Location	chr3:136139730-136139731
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10804640	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10935181	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10935182	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10935183	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10935184	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11717954	0.91[AMR][1000 genomes]
rs12492510	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1279424	0.81[EUR][1000 genomes]
rs480162	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs517319	0.85[AFR][1000 genomes]
rs521746	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs527888	0.84[EUR][1000 genomes]
rs556788	0.82[EUR][1000 genomes]
rs56235965	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs619605	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs654237	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs655748	0.80[AMR][1000 genomes]
rs655836	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66691851	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6791611	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs684195	0.80[EUR][1000 genomes]
rs696518	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs696520	0.85[EUR][1000 genomes]
rs698269	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs711972	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73222302	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs833861	0.81[EUR][1000 genomes]
rs834304	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs834305	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs864437	0.86[AMR][1000 genomes]
rs866758	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
10	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11915629	PCCB	cis	multi-tissue	Pritchard
rs11915629	PCCB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136054600-136172000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:136069800-136159600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:136075800-136160200	Weak transcription	Brain Germinal Matrix	brain
4	chr3:136079400-136174200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr3:136085800-136174800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:136086200-136174800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:136110800-136174200	Weak transcription	Esophagus	oesophagus
8	chr3:136112200-136174200	Weak transcription	Osteobl	bone
9	chr3:136113000-136174200	Weak transcription	Aorta	Aorta
10	chr3:136114400-136139800	Weak transcription	NHDF-Ad	bronchial
11	chr3:136114800-136160400	Weak transcription	Fetal Kidney	kidney
12	chr3:136115400-136174200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr3:136116200-136173400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:136116600-136174400	Weak transcription	Hela-S3	cervix
15	chr3:136118200-136170400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:136123000-136157000	Weak transcription	Colonic Mucosa	Colon
17	chr3:136124000-136141600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:136124600-136174000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:136127400-136140000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:136129800-136141400	Weak transcription	Brain Substantia Nigra	brain
21	chr3:136129800-136174200	Weak transcription	HSMMtube	muscle
22	chr3:136131000-136160200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:136131400-136160400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:136131400-136175400	Weak transcription	HMEC	breast
25	chr3:136132000-136145400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:136132800-136142000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:136132800-136142000	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr3:136133000-136142000	Strong transcription	Dnd41	blood
29	chr3:136133000-136160400	Weak transcription	Spleen	Spleen
30	chr3:136133200-136173800	Weak transcription	Fetal Heart	heart
31	chr3:136133600-136141000	Strong transcription	Fetal Stomach	stomach
32	chr3:136133600-136173400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr3:136133800-136140800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:136134200-136141000	Strong transcription	Placenta	Placenta
35	chr3:136134400-136141000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:136134600-136140800	Weak transcription	A549	lung
37	chr3:136135000-136141400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:136135200-136142000	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:136135200-136173400	Weak transcription	NHEK	skin
40	chr3:136135800-136140000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:136136400-136141400	Strong transcription	Fetal Intestine Large	intestine
42	chr3:136136600-136140600	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr3:136136800-136140000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:136136800-136140000	Strong transcription	Fetal Intestine Small	intestine
45	chr3:136137600-136141400	Strong transcription	Fetal Muscle Leg	muscle
46	chr3:136137600-136141800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:136137600-136141800	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr3:136137600-136141800	Strong transcription	Fetal Thymus	thymus
49	chr3:136137800-136139800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr3:136137800-136140400	Strong transcription	Duodenum Smooth Muscle	Duodenum

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