Variant report

Variant	rs2381541
Chromosome Location	chr9:7057701-7057702
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	chr9:7051581..7054293-chr9:7055466..7057984,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10739114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10815511	0.95[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1093703	0.88[JPT][hapmap]
rs1093705	0.88[JPT][hapmap]
rs10975997	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs10976029	0.80[CEU][hapmap]
rs1544055	0.87[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1570509	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1570513	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2381540	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2381542	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2381544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2381545	0.90[CEU][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs3898792	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4523317	0.87[EUR][1000 genomes]
rs4641121	0.90[CEU][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs4742294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742296	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4742298	0.85[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4742300	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4742302	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4742305	0.89[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6477142	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6477143	0.95[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6477144	0.95[CEU][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6477147	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6477149	0.95[CEU][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6477150	0.89[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7027561	0.86[GIH][hapmap]
rs7031179	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7037803	0.86[GIH][hapmap]
rs7852014	0.88[JPT][hapmap]
rs7858761	0.95[CEU][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs864696	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs866566	0.95[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv831501	chr9:6868099-7058526	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	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
6	nsv870178	chr9:6941584-7060029	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	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
8	nsv1024763	chr9:7022554-7061314	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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
13	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2381541	JMJD2C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 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	chr9:7018800-7064400	Weak transcription	Psoas Muscle	Psoas
8	chr9:7028400-7076800	Weak transcription	Placenta	Placenta
9	chr9:7028800-7076400	Weak transcription	Aorta	Aorta
10	chr9:7028800-7077000	Weak transcription	Esophagus	oesophagus
11	chr9:7028800-7086400	Weak transcription	Right Ventricle	heart
12	chr9:7029000-7061400	Weak transcription	Fetal Intestine Small	intestine
13	chr9:7029000-7076400	Weak transcription	Ovary	ovary
14	chr9:7029000-7076600	Weak transcription	Lung	lung
15	chr9:7029000-7077400	Weak transcription	Gastric	stomach
16	chr9:7029000-7081200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:7034000-7103600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr9:7043000-7069400	Weak transcription	NHDF-Ad	bronchial
19	chr9:7043400-7103600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr9:7045000-7059200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr9:7045400-7077000	Weak transcription	Fetal Muscle Leg	muscle
22	chr9:7045400-7077000	Weak transcription	HMEC	breast
23	chr9:7046400-7077000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr9:7047600-7061400	Weak transcription	Spleen	Spleen
25	chr9:7049200-7075600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr9:7049400-7076000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr9:7050000-7076800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr9:7050000-7082200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr9:7050200-7076600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr9:7050400-7061400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr9:7050400-7076400	Weak transcription	Dnd41	blood
32	chr9:7051000-7068600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:7051600-7103200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr9:7051800-7076200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr9:7052000-7057800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr9:7052000-7057800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr9:7052000-7057800	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr9:7052000-7057800	Weak transcription	Adipose Nuclei	Adipose
39	chr9:7052000-7064000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr9:7052000-7074800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr9:7052000-7075800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr9:7052000-7076400	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr9:7052200-7057800	Weak transcription	Liver	Liver
44	chr9:7052600-7086400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr9:7053000-7060200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr9:7053000-7076200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr9:7053000-7076200	Weak transcription	Stomach Smooth Muscle	stomach
48	chr9:7053000-7086600	Weak transcription	Fetal Intestine Large	intestine
49	chr9:7053200-7058200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr9:7053200-7076600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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