Variant report

Variant	rs12107768
Chromosome Location	chr3:50063753-50063754
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:50037509..50039299-chr3:50062748..50064702,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1061474	0.88[ASN][1000 genomes]
rs1138536	0.88[ASN][1000 genomes]
rs11714324	0.82[AMR][1000 genomes]
rs12634780	0.85[ASN][1000 genomes]
rs13077403	0.82[ASN][1000 genomes]
rs13079006	0.81[ASN][1000 genomes]
rs13082703	0.85[ASN][1000 genomes]
rs17657664	0.85[ASN][1000 genomes]
rs17657688	0.85[ASN][1000 genomes]
rs2240328	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2247510	0.92[ASN][1000 genomes]
rs2352969	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2526747	0.98[ASN][1000 genomes]
rs2526749	0.95[ASN][1000 genomes]
rs2526750	0.92[ASN][1000 genomes]
rs2624815	0.98[ASN][1000 genomes]
rs2624817	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2624819	0.82[ASN][1000 genomes]
rs2624821	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2624822	0.95[ASN][1000 genomes]
rs2624826	0.88[ASN][1000 genomes]
rs2624832	0.85[ASN][1000 genomes]
rs2624834	0.97[ASN][1000 genomes]
rs2624848	0.88[ASN][1000 genomes]
rs2681776	0.85[ASN][1000 genomes]
rs2681779	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2856237	0.88[ASN][1000 genomes]
rs2856238	0.88[ASN][1000 genomes]
rs34312088	0.85[ASN][1000 genomes]
rs3774734	0.95[ASN][1000 genomes]
rs4688688	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4688753	0.98[ASN][1000 genomes]
rs4688754	0.98[ASN][1000 genomes]
rs6446192	0.82[ASN][1000 genomes]
rs6446194	0.92[ASN][1000 genomes]
rs6446195	0.98[ASN][1000 genomes]
rs6446197	0.93[ASN][1000 genomes]
rs6762477	0.98[ASN][1000 genomes]
rs6793528	0.98[ASN][1000 genomes]
rs6799579	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808044	0.87[ASN][1000 genomes]
rs7061	0.95[ASN][1000 genomes]
rs7430334	0.98[ASN][1000 genomes]
rs7634441	0.98[ASN][1000 genomes]
rs7648174	0.85[ASN][1000 genomes]
rs9682295	0.98[ASN][1000 genomes]
rs9844201	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv834689	chr3:49962930-50085119	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1012903	chr3:49978765-50071878	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv460527	chr3:50028385-50153356	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv590249	chr3:50028385-50153356	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12107768	RBM6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49998000-50078200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:49998400-50078600	Weak transcription	K562	blood
3	chr3:50006000-50064000	Weak transcription	Stomach Mucosa	stomach
4	chr3:50010800-50087000	Weak transcription	NHLF	lung
5	chr3:50011000-50078400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:50011000-50091600	Weak transcription	Colonic Mucosa	Colon
7	chr3:50015200-50092000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:50028800-50082600	Weak transcription	Right Ventricle	heart
9	chr3:50030200-50065600	Weak transcription	Fetal Heart	heart
10	chr3:50036600-50085600	Weak transcription	HUVEC	blood vessel
11	chr3:50037200-50087000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:50038400-50084600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr3:50038600-50087400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:50039400-50084600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:50041400-50095200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:50041600-50065200	Weak transcription	NH-A	brain
17	chr3:50041600-50085000	Weak transcription	Fetal Brain Female	brain
18	chr3:50041600-50085400	Weak transcription	Brain Angular Gyrus	brain
19	chr3:50041600-50093400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:50041800-50085200	Weak transcription	Fetal Brain Male	brain
21	chr3:50043400-50085200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:50045200-50085000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:50046800-50064600	Weak transcription	Aorta	Aorta
24	chr3:50046800-50065400	Weak transcription	Fetal Kidney	kidney
25	chr3:50046800-50085800	Weak transcription	HMEC	breast
26	chr3:50047200-50085200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:50047200-50085400	Weak transcription	Left Ventricle	heart
28	chr3:50047200-50092600	Weak transcription	Gastric	stomach
29	chr3:50047400-50085000	Weak transcription	Lung	lung
30	chr3:50048800-50085600	Weak transcription	A549	lung
31	chr3:50049800-50084000	Weak transcription	Brain Germinal Matrix	brain
32	chr3:50050600-50066000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:50051400-50084600	Weak transcription	Spleen	Spleen
34	chr3:50051600-50095200	Weak transcription	Pancreas	Pancrea
35	chr3:50051800-50085000	Weak transcription	Brain Anterior Caudate	brain
36	chr3:50051800-50085400	Weak transcription	Brain Hippocampus Middle	brain
37	chr3:50052200-50084800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:50052200-50087000	Weak transcription	NHDF-Ad	bronchial
39	chr3:50052400-50085600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr3:50053200-50064800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:50053200-50065600	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr3:50055600-50084200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:50055600-50085600	Weak transcription	Hela-S3	cervix
44	chr3:50056000-50066000	Strong transcription	Fetal Thymus	thymus
45	chr3:50056400-50114400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:50056800-50078400	Weak transcription	Ovary	ovary
47	chr3:50057000-50071600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:50057000-50073400	Weak transcription	Thymus	Thymus
49	chr3:50057000-50085400	Weak transcription	Fetal Lung	lung
50	chr3:50057200-50064800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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