Variant report

Variant	rs2694398
Chromosome Location	chr12:105956692-105956693
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	chr12:105944792..105946780-chr12:105955206..105957369,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C12orf75-6	chr12:105955031-105962713	NONHSAT030458

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10735407	0.82[ASN][1000 genomes]
rs10861456	0.81[AMR][1000 genomes]
rs10861457	0.81[AMR][1000 genomes]
rs10861461	0.83[ASN][1000 genomes]
rs11112595	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11112596	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1317555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1526844	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1526846	0.86[ASN][1000 genomes]
rs1806811	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1997174	0.81[AMR][1000 genomes]
rs2049571	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2049572	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2374514	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2374515	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2694388	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2694390	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2694394	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2694395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2694399	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2694400	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2694401	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2694404	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2711732	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2711734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2711735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2711736	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2711737	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2711739	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2711741	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2888859	0.92[ASN][1000 genomes]
rs4468444	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs876929	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941105	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832507	chr12:105821685-106005186	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1039068	chr12:105935786-106211250	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105938800-105964600	Weak transcription	Aorta	Aorta
2	chr12:105954600-105957400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:105955000-105958000	Enhancers	Fetal Muscle Leg	muscle
4	chr12:105955200-105956800	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr12:105955200-105957200	Enhancers	HMEC	breast
6	chr12:105955400-105956800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:105955400-105956800	Enhancers	Colon Smooth Muscle	Colon
8	chr12:105955400-105956800	Enhancers	Fetal Heart	heart
9	chr12:105955400-105957000	Enhancers	Fetal Stomach	stomach
10	chr12:105955400-105957000	Flanking Active TSS	Hela-S3	cervix
11	chr12:105955400-105958200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:105955600-105956800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:105955600-105957000	Enhancers	H9 Cell Line	embryonic stem cell
14	chr12:105955800-105956800	Enhancers	Adipose Nuclei	Adipose
15	chr12:105955800-105957000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr12:105955800-105957000	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr12:105955800-105957000	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr12:105956000-105956800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:105956000-105957000	Flanking Active TSS	Fetal Muscle Trunk	muscle
20	chr12:105956200-105956800	Enhancers	Fetal Brain Female	brain
21	chr12:105956400-105956800	Enhancers	Brain Germinal Matrix	brain
22	chr12:105956400-105956800	Flanking Active TSS	NH-A	brain
23	chr12:105956400-105957000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:105956400-105957000	Flanking Active TSS	HSMM	muscle
25	chr12:105956400-105958000	Weak transcription	HUVEC	blood vessel
26	chr12:105956400-105967400	Weak transcription	Left Ventricle	heart
27	chr12:105956600-105956800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr12:105956600-105956800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:105956600-105956800	Flanking Active TSS	HSMMtube	muscle
30	chr12:105956600-105956800	Flanking Active TSS	NHEK	skin
31	chr12:105956600-105957000	Enhancers	Colonic Mucosa	Colon
32	chr12:105956600-105957000	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr12:105956600-105957000	Enhancers	NHLF	lung
34	chr12:105956600-105957000	Enhancers	Osteobl	bone
35	chr12:105956600-105957200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr12:105956600-105957200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:105956600-105957200	Flanking Active TSS	A549	lung
38	chr12:105956600-105957400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:105956600-105979000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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