Variant report

Variant	rs595532
Chromosome Location	chr3:136053963-136053964
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	chr3:136044505..136047310-chr3:136053454..136056821,3	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1070232	0.93[JPT][hapmap]
rs10935182	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs10935183	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs10935184	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs1145106	0.87[JPT][hapmap]
rs1153877	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs11715257	0.87[JPT][hapmap]
rs11717954	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs12492510	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs1279086	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs1279425	0.93[JPT][hapmap]
rs1279831	0.92[CHB][hapmap]
rs1279840	0.93[JPT][hapmap]
rs1394092	0.93[JPT][hapmap]
rs1711161	0.81[JPT][hapmap]
rs1711171	0.93[JPT][hapmap]
rs2655008	0.87[JPT][hapmap]
rs3755636	0.93[JPT][hapmap]
rs4678428	0.93[JPT][hapmap]
rs483465	0.93[JPT][hapmap]
rs518972	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs521746	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs548288	0.93[JPT][hapmap]
rs553018	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs556788	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs571513	0.93[JPT][hapmap]
rs576771	0.87[JPT][hapmap]
rs589092	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs606725	0.93[JPT][hapmap]
rs619605	0.86[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs650326	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs654237	0.83[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs655836	0.83[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs667920	0.93[JPT][hapmap]
rs6791611	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs695983	0.87[JPT][hapmap]
rs696081	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs696516	0.87[JPT][hapmap]
rs696518	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs696520	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs698270	0.87[JPT][hapmap]
rs699165	0.93[JPT][hapmap]
rs711975	0.87[JPT][hapmap]
rs7372313	0.92[CHB][hapmap];1.00[YRI][hapmap]
rs7620314	0.92[CHB][hapmap]
rs834304	0.92[CHB][hapmap]
rs864437	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs866758	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs900048	0.87[JPT][hapmap]
rs9845457	0.83[CHB][hapmap]
rs9854084	0.93[JPT][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	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	nsv4025	chr3:136017458-136065622	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs595532	PCCB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135999800-136061200	Weak transcription	Hela-S3	cervix
2	chr3:136032800-136055400	Weak transcription	HUVEC	blood vessel
3	chr3:136039000-136072400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:136039200-136062400	Weak transcription	Fetal Heart	heart
5	chr3:136040400-136062800	Weak transcription	Stomach Mucosa	stomach
6	chr3:136040600-136061400	Weak transcription	Small Intestine	intestine
7	chr3:136042400-136058200	Weak transcription	Psoas Muscle	Psoas
8	chr3:136042400-136078800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr3:136042600-136072600	Strong transcription	Dnd41	blood
10	chr3:136043400-136098600	Weak transcription	Fetal Brain Male	brain
11	chr3:136043600-136082000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:136043800-136070400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:136044800-136054600	Strong transcription	Brain Inferior Temporal Lobe	brain
14	chr3:136045200-136060800	Strong transcription	Liver	Liver
15	chr3:136045200-136062000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:136045600-136079200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:136046200-136060000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:136047600-136098000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr3:136047800-136068200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:136047800-136074800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr3:136048000-136054200	Weak transcription	HMEC	breast
22	chr3:136048200-136060200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr3:136048400-136062800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:136048800-136062600	Weak transcription	NHEK	skin
25	chr3:136049000-136056000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:136049000-136062800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:136050800-136054200	Strong transcription	Brain Hippocampus Middle	brain
28	chr3:136050800-136062800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:136051000-136054800	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:136051000-136062200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:136051000-136062400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:136051000-136062800	Strong transcription	Adipose Nuclei	Adipose
33	chr3:136051000-136063600	Strong transcription	Fetal Thymus	thymus
34	chr3:136051000-136069800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:136051200-136063600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:136051400-136054600	Strong transcription	Brain Angular Gyrus	brain
37	chr3:136051400-136055000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr3:136051600-136054600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:136051600-136055400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:136051600-136055600	Strong transcription	Fetal Intestine Small	intestine
41	chr3:136051600-136055600	Strong transcription	Fetal Stomach	stomach
42	chr3:136051600-136055600	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:136051600-136055800	Strong transcription	Fetal Muscle Leg	muscle
44	chr3:136051600-136057000	Strong transcription	GM12878-XiMat	blood
45	chr3:136051600-136063600	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr3:136051600-136063600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:136051600-136064800	Strong transcription	Primary T cells from cord blood	blood
48	chr3:136051600-136069200	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr3:136051600-136070800	Strong transcription	Fetal Muscle Trunk	muscle
50	chr3:136051800-136060400	Strong transcription	Fetal Brain Female	brain

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