Variant report

Variant	rs12630999
Chromosome Location	chr3:136300927-136300928
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	chr3:136279189..136281857-chr3:136298738..136300966,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1017881	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1070230	0.86[EUR][1000 genomes]
rs1070232	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10935182	0.93[JPT][hapmap]
rs10935183	0.87[JPT][hapmap]
rs10935184	1.00[JPT][hapmap]
rs10935186	0.93[JPT][hapmap]
rs1145106	0.84[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap]
rs11715257	0.96[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap]
rs11717954	0.87[JPT][hapmap]
rs11919030	0.93[JPT][hapmap]
rs12492510	0.87[JPT][hapmap]
rs12635723	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12637102	0.80[EUR][1000 genomes]
rs13068119	0.88[MEX][hapmap]
rs1394092	0.86[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs1681818	0.86[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap]
rs1729951	0.87[JPT][hapmap]
rs2062322	0.93[JPT][hapmap]
rs2655008	0.93[JPT][hapmap]
rs34553037	0.83[MEX][hapmap]
rs34602896	0.88[MEX][hapmap]
rs34967300	0.88[MEX][hapmap]
rs34992220	0.87[CHD][hapmap]
rs3856637	0.86[ASW][hapmap];0.90[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes]
rs4038578	0.93[JPT][hapmap]
rs4408829	0.93[JPT][hapmap]
rs4456810	0.84[AMR][1000 genomes]
rs4521165	1.00[JPT][hapmap]
rs4678433	0.86[ASW][hapmap];0.95[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.87[ASN][1000 genomes]
rs4678437	0.90[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4678438	0.90[CEU][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs521746	0.87[JPT][hapmap]
rs57693506	0.83[ASN][1000 genomes]
rs6439646	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6439649	1.00[JPT][hapmap]
rs6784582	0.80[AMR][1000 genomes]
rs6791142	0.93[JPT][hapmap]
rs6791611	0.87[JPT][hapmap]
rs6794351	0.95[CEU][hapmap];0.80[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6802702	0.93[JPT][hapmap]
rs6808312	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs696518	0.93[JPT][hapmap]
rs698270	0.90[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs699165	0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap]
rs711975	0.93[JPT][hapmap]
rs7432375	0.93[JPT][hapmap]
rs7616204	0.93[JPT][hapmap]
rs7618518	1.00[JPT][hapmap]
rs7618871	0.93[JPT][hapmap]
rs7621025	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs833752	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs834304	0.85[JPT][hapmap]
rs864437	0.87[JPT][hapmap]
rs866758	0.87[JPT][hapmap]
rs900048	0.86[ASW][hapmap];0.90[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap]
rs900818	0.93[JPT][hapmap]
rs9289511	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs940174	0.93[JPT][hapmap]
rs9811416	0.82[ASN][1000 genomes]
rs9820485	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs9821478	0.83[ASN][1000 genomes]
rs9833207	0.90[CHB][hapmap];0.87[CHD][hapmap]
rs9836231	0.93[JPT][hapmap]
rs9845762	0.90[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes]
rs9851986	0.90[CHB][hapmap];0.87[CHD][hapmap]
rs9854084	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs9869720	0.90[CHB][hapmap]
rs9883916	0.88[MEX][hapmap]

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	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
2	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
3	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
4	nsv877523	chr3:136088038-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv520012	chr3:136088038-136314119	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv877525	chr3:136112109-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv877526	chr3:136149139-136310985	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv877527	chr3:136182053-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv1794138	chr3:136300732-136332204	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12630999	MSL2	cis	cerebellum	SCAN
rs12630999	NCK1	cis	parietal	SCAN
rs12630999	PCCB	cis	lymphoblastoid	seeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136176400-136314200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:136212200-136323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:136213000-136326600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:136247200-136319800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:136247200-136334800	Weak transcription	Aorta	Aorta
6	chr3:136248200-136349200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:136251400-136319000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:136251600-136322400	Weak transcription	Liver	Liver
9	chr3:136252600-136320400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:136252800-136305600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:136252800-136314800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:136263000-136327200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:136265400-136314800	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:136266400-136315600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr3:136266600-136314600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:136266600-136316200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:136266800-136314800	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr3:136268200-136351200	Weak transcription	Esophagus	oesophagus
19	chr3:136269000-136303200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr3:136271200-136331400	Weak transcription	NHDF-Ad	bronchial
21	chr3:136272600-136335600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:136274200-136314000	Weak transcription	GM12878-XiMat	blood
23	chr3:136276600-136303800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:136277800-136315200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr3:136279800-136303200	Weak transcription	Ovary	ovary
26	chr3:136280000-136323000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:136283600-136314600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr3:136283800-136341800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:136284400-136337800	Weak transcription	Fetal Kidney	kidney
30	chr3:136285000-136307200	Weak transcription	Lung	lung
31	chr3:136285000-136314800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:136285200-136335400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:136285400-136313600	Weak transcription	Left Ventricle	heart
34	chr3:136285800-136303400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:136286400-136305200	Weak transcription	Fetal Thymus	thymus
36	chr3:136286600-136314600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:136286800-136307200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:136286800-136322600	Weak transcription	Placenta	Placenta
39	chr3:136286800-136343600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr3:136287200-136335400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr3:136287400-136305200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr3:136288000-136304800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:136289600-136341800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:136290000-136351600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:136290400-136305600	Weak transcription	Gastric	stomach
46	chr3:136290400-136315000	Weak transcription	Primary B cells from peripheral blood	blood
47	chr3:136292000-136307000	Weak transcription	Fetal Muscle Leg	muscle
48	chr3:136292200-136307200	Weak transcription	Thymus	Thymus
49	chr3:136292400-136303400	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr3:136293000-136306000	Weak transcription	Fetal Stomach	stomach

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