Variant report

Variant	rs6477143
Chromosome Location	chr9:7067411-7067412
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	chr9:7062837..7065514-chr9:7066672..7068819,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10739114	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10815511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1093703	0.83[JPT][hapmap]
rs1093705	0.83[JPT][hapmap]
rs10975997	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10976029	0.81[CEU][hapmap]
rs1544055	0.94[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1570509	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1570513	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2381540	1.00[CEU][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2381541	0.95[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2381542	0.90[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2381544	0.95[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2381545	0.85[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3898792	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4523317	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4641121	0.85[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4742294	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4742296	0.95[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4742298	0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4742300	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4742302	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4742305	0.84[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6477142	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6477144	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6477147	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6477149	0.90[CEU][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6477150	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7031179	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes]
rs7852014	0.82[JPT][hapmap]
rs7858761	0.91[CEU][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs864696	0.86[EUR][1000 genomes]
rs866566	1.00[CEU][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv892181	chr9:6680477-7070962	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
3	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv892185	chr9:6929053-7070962	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv892186	chr9:6942605-7075305	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv466117	chr9:7030268-7084558	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv613258	chr9:7030268-7084558	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv613259	chr9:7032776-7541338	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv1015874	chr9:7048807-7434890	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	nsv539971	chr9:7048807-7434890	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
11	nsv523788	chr9:7064934-7075305	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6477143	JMJD2C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:7009000-7076600	Weak transcription	HSMM	muscle
2	chr9:7009200-7077600	Weak transcription	Osteobl	bone
3	chr9:7009800-7076600	Weak transcription	HSMMtube	muscle
4	chr9:7012200-7111200	Weak transcription	Colonic Mucosa	Colon
5	chr9:7012800-7076800	Weak transcription	Pancreas	Pancrea
6	chr9:7017800-7075000	Weak transcription	HepG2	liver
7	chr9:7028400-7076800	Weak transcription	Placenta	Placenta
8	chr9:7028800-7076400	Weak transcription	Aorta	Aorta
9	chr9:7028800-7077000	Weak transcription	Esophagus	oesophagus
10	chr9:7028800-7086400	Weak transcription	Right Ventricle	heart
11	chr9:7029000-7076400	Weak transcription	Ovary	ovary
12	chr9:7029000-7076600	Weak transcription	Lung	lung
13	chr9:7029000-7077400	Weak transcription	Gastric	stomach
14	chr9:7029000-7081200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr9:7034000-7103600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr9:7043000-7069400	Weak transcription	NHDF-Ad	bronchial
17	chr9:7043400-7103600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr9:7045400-7077000	Weak transcription	Fetal Muscle Leg	muscle
19	chr9:7045400-7077000	Weak transcription	HMEC	breast
20	chr9:7046400-7077000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr9:7049200-7075600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr9:7049400-7076000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr9:7050000-7076800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr9:7050000-7082200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr9:7050200-7076600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr9:7050400-7076400	Weak transcription	Dnd41	blood
27	chr9:7051000-7068600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr9:7051600-7103200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr9:7051800-7076200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr9:7052000-7074800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:7052000-7075800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr9:7052000-7076400	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr9:7052600-7086400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr9:7053000-7076200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr9:7053000-7076200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr9:7053000-7086600	Weak transcription	Fetal Intestine Large	intestine
37	chr9:7053200-7076600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr9:7053200-7077000	Weak transcription	Brain Angular Gyrus	brain
39	chr9:7053200-7084400	Weak transcription	Brain Hippocampus Middle	brain
40	chr9:7053200-7099200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr9:7054400-7077400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr9:7055200-7069000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr9:7055600-7076000	Weak transcription	Left Ventricle	heart
44	chr9:7055600-7076200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr9:7056200-7074800	Weak transcription	GM12878-XiMat	blood
46	chr9:7056400-7076000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr9:7058000-7074800	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr9:7058400-7076400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr9:7058400-7076400	Weak transcription	Liver	Liver
50	chr9:7058400-7088600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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