Variant report

Variant	rs9848883
Chromosome Location	chr3:136008432-136008433
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135793633..135795378-chr3:136008278..136010126,2	MCF-7	breast:
2	chr3:135911672..135913999-chr3:136007331..136010292,2	K562	blood:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1145106	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs1154988	0.88[CHB][hapmap]
rs12163608	0.83[EUR][1000 genomes]
rs12330258	0.85[ASN][1000 genomes]
rs12330635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1279425	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1279840	1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[ASN][1000 genomes]
rs1291921	0.89[ASN][1000 genomes]
rs1394092	0.89[CHB][hapmap]
rs1618069	0.91[ASN][1000 genomes]
rs1711171	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[ASN][1000 genomes]
rs3755636	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs4678428	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[ASN][1000 genomes]
rs483465	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[ASN][1000 genomes]
rs548288	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[ASN][1000 genomes]
rs553018	0.86[JPT][hapmap]
rs571513	0.89[CHB][hapmap]
rs576771	0.91[CHD][hapmap];0.83[ASN][1000 genomes]
rs606725	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs61789644	1.00[AFR][1000 genomes]
rs61789645	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61789646	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61789652	1.00[AMR][1000 genomes]
rs632016	0.84[ASN][1000 genomes]
rs645040	0.88[CHB][hapmap]
rs650505	0.87[ASN][1000 genomes]
rs665200	0.88[ASN][1000 genomes]
rs667920	0.89[CHB][hapmap];0.84[CHD][hapmap];0.88[ASN][1000 genomes]
rs6770476	0.92[ASN][1000 genomes]
rs684773	0.88[CHB][hapmap]
rs687339	0.88[CHB][hapmap]
rs695983	0.89[CHB][hapmap];0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs696516	0.84[CHD][hapmap]
rs698270	0.89[CHB][hapmap]
rs72493178	0.94[ASN][1000 genomes]
rs73222262	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7620314	0.92[JPT][hapmap]
rs7628146	0.88[ASN][1000 genomes]
rs9289509	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs9809427	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9826198	1.00[AFR][1000 genomes]
rs9832056	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9832556	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9832813	0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9833010	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs9835523	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9840812	0.88[CHB][hapmap]
rs9845396	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9851986	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9852811	1.00[AFR][1000 genomes]
rs9854084	0.89[CHB][hapmap]
rs9854328	0.87[ASN][1000 genomes]
rs9856769	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864407	1.00[AFR][1000 genomes]
rs9869720	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv508246	chr3:135922023-136038622	Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9848883	PCCB	cis	lymphoblastoid	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135970600-136039400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:135976200-136012400	Weak transcription	NHLF	lung
3	chr3:135976200-136016400	Weak transcription	Colonic Mucosa	Colon
4	chr3:135976200-136021600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:135981200-136052000	Weak transcription	NH-A	brain
6	chr3:135981600-136020400	Weak transcription	HUVEC	blood vessel
7	chr3:135996800-136016000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:135997000-136010600	Weak transcription	Gastric	stomach
9	chr3:135997000-136012000	Weak transcription	Spleen	Spleen
10	chr3:135997400-136015200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:135998000-136040200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:135999800-136013000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:135999800-136013000	Weak transcription	Small Intestine	intestine
14	chr3:135999800-136016200	Weak transcription	Esophagus	oesophagus
15	chr3:135999800-136016800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:135999800-136019000	Weak transcription	NHEK	skin
17	chr3:135999800-136038200	Weak transcription	Fetal Brain Male	brain
18	chr3:135999800-136061200	Weak transcription	Hela-S3	cervix
19	chr3:136000000-136016600	Weak transcription	Thymus	Thymus
20	chr3:136000000-136024600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr3:136000200-136012200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:136000200-136038200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr3:136001200-136011400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr3:136001200-136016400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:136001200-136019200	Weak transcription	Colon Smooth Muscle	Colon
26	chr3:136002000-136017400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:136002200-136012400	Weak transcription	Brain Angular Gyrus	brain
28	chr3:136002200-136014800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:136002200-136015600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr3:136002400-136009400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr3:136002400-136010400	Weak transcription	Psoas Muscle	Psoas
32	chr3:136002400-136012000	Weak transcription	Pancreas	Pancrea
33	chr3:136002600-136010200	Weak transcription	Fetal Heart	heart
34	chr3:136002800-136012600	Weak transcription	GM12878-XiMat	blood
35	chr3:136003000-136012200	Weak transcription	Aorta	Aorta
36	chr3:136003000-136016400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:136004200-136016000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:136004200-136016200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr3:136004400-136012600	Weak transcription	A549	lung
40	chr3:136004400-136014000	Weak transcription	K562	blood
41	chr3:136004400-136015600	Weak transcription	Fetal Lung	lung
42	chr3:136004600-136011400	Weak transcription	Fetal Kidney	kidney
43	chr3:136004600-136012200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr3:136004600-136012200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr3:136004600-136012200	Weak transcription	Brain Hippocampus Middle	brain
46	chr3:136004600-136012200	Weak transcription	HSMMtube	muscle
47	chr3:136004600-136012600	Weak transcription	Fetal Thymus	thymus
48	chr3:136004600-136012600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr3:136004600-136014000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:136004600-136021400	Weak transcription	HMEC	breast

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