Variant report

Variant	rs619605
Chromosome Location	chr3:136087012-136087013
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136085761..136088566-chr3:136470764..136472314,2	K562	blood:

Variant related genes	Relation type
ENSG00000261758	Chromatin interaction
ENSG00000118007	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1070232	0.93[JPT][hapmap]
rs10804640	0.82[EUR][1000 genomes]
rs10935181	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10935182	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10935183	0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs10935184	0.86[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes]
rs1145106	1.00[JPT][hapmap]
rs1153877	0.84[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs1154988	0.81[JPT][hapmap]
rs11715257	1.00[JPT][hapmap]
rs11717954	0.85[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11915629	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12492510	0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs1279086	0.85[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1279424	0.83[AMR][1000 genomes]
rs1279425	0.93[JPT][hapmap]
rs1279831	0.80[JPT][hapmap]
rs1279840	0.93[JPT][hapmap]
rs1394092	0.93[JPT][hapmap]
rs1711161	0.94[JPT][hapmap]
rs1711170	0.81[JPT][hapmap]
rs1711171	0.93[JPT][hapmap]
rs2655008	1.00[JPT][hapmap]
rs3755636	0.93[JPT][hapmap]
rs3957816	0.81[JPT][hapmap]
rs4678428	0.93[JPT][hapmap]
rs4678433	0.93[JPT][hapmap]
rs480162	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs480330	0.80[ASN][1000 genomes]
rs483465	0.93[JPT][hapmap]
rs517319	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs518972	0.85[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs521746	0.96[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs527888	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs548288	0.93[JPT][hapmap]
rs553018	0.86[CHB][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs556788	0.85[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56235965	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs570621	0.82[AMR][1000 genomes]
rs571513	0.93[JPT][hapmap]
rs576771	0.87[JPT][hapmap]
rs589092	0.85[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs595532	0.86[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs606725	0.93[JPT][hapmap]
rs645040	0.81[JPT][hapmap]
rs650326	0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs654237	0.96[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs655748	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs655836	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs661739	0.81[JPT][hapmap]
rs664088	0.85[AMR][1000 genomes]
rs667920	0.93[JPT][hapmap]
rs6791611	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs681783	0.86[AMR][1000 genomes]
rs684773	0.81[JPT][hapmap]
rs687339	0.81[JPT][hapmap]
rs695983	1.00[JPT][hapmap]
rs696081	0.85[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs696516	1.00[JPT][hapmap]
rs696518	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs696520	0.93[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs698269	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs698270	1.00[JPT][hapmap]
rs699165	0.93[JPT][hapmap]
rs711972	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs711975	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs73222302	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7620314	0.92[CHB][hapmap]
rs7621025	0.93[JPT][hapmap]
rs833752	0.93[JPT][hapmap]
rs834304	0.85[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs834305	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs838202	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs864437	0.85[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs866758	0.80[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs895894	0.81[JPT][hapmap]
rs900048	1.00[JPT][hapmap]
rs9845457	0.81[JPT][hapmap]
rs9854084	0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs619605	PCCB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136043400-136098600	Weak transcription	Fetal Brain Male	brain
2	chr3:136047600-136098000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:136054600-136172000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:136055600-136100800	Weak transcription	Spleen	Spleen
5	chr3:136063400-136139000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:136063400-136139000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:136063600-136097000	Weak transcription	Colonic Mucosa	Colon
8	chr3:136063600-136105600	Weak transcription	Gastric	stomach
9	chr3:136063600-136110600	Weak transcription	Small Intestine	intestine
10	chr3:136063600-136139200	Weak transcription	Pancreas	Pancrea
11	chr3:136063800-136095200	Weak transcription	Lung	lung
12	chr3:136065400-136097200	Weak transcription	HepG2	liver
13	chr3:136067600-136109000	Weak transcription	HUVEC	blood vessel
14	chr3:136068600-136103800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:136069400-136121200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:136069600-136107400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:136069600-136138800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:136069600-136139400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:136069800-136088800	Weak transcription	HMEC	breast
20	chr3:136069800-136106600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:136069800-136118800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:136069800-136159600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:136070400-136095000	Weak transcription	NH-A	brain
24	chr3:136070600-136101000	Weak transcription	Right Ventricle	heart
25	chr3:136070600-136105800	Weak transcription	Psoas Muscle	Psoas
26	chr3:136070800-136095200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:136070800-136096800	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:136070800-136096800	Weak transcription	HSMMtube	muscle
29	chr3:136070800-136099600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:136070800-136112200	Weak transcription	Aorta	Aorta
31	chr3:136070800-136121400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:136072600-136098800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:136072800-136097000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:136072800-136100400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:136073000-136093800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:136075000-136137800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:136075400-136093600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:136075400-136093800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr3:136075400-136108000	Weak transcription	Fetal Brain Female	brain
40	chr3:136075600-136094200	Weak transcription	Left Ventricle	heart
41	chr3:136075600-136097000	Weak transcription	Fetal Lung	lung
42	chr3:136075600-136105800	Weak transcription	Ovary	ovary
43	chr3:136075800-136094200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:136075800-136099000	Weak transcription	Fetal Muscle Leg	muscle
45	chr3:136075800-136160200	Weak transcription	Brain Germinal Matrix	brain
46	chr3:136076600-136088800	Strong transcription	Dnd41	blood
47	chr3:136078200-136096000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr3:136078600-136087800	Weak transcription	Thymus	Thymus
49	chr3:136079400-136174200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:136081200-136093600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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