Variant report

Variant	rs73297243
Chromosome Location	chr12:49847630-49847631
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	chr12:49847113..49848720-chr12:49850682..49852542,2	MCF-7	breast:
2	chr12:49760155..49761819-chr12:49847240..49849852,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10160947	0.83[ASN][1000 genomes]
rs10161131	0.83[ASN][1000 genomes]
rs10506284	1.00[ASN][1000 genomes]
rs11168988	1.00[ASN][1000 genomes]
rs11169015	1.00[ASN][1000 genomes]
rs11169016	1.00[ASN][1000 genomes]
rs11169017	1.00[ASN][1000 genomes]
rs11169027	1.00[ASN][1000 genomes]
rs11611743	1.00[ASN][1000 genomes]
rs11834161	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299282	1.00[ASN][1000 genomes]
rs12301632	1.00[ASN][1000 genomes]
rs12302036	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12306118	1.00[ASN][1000 genomes]
rs12306212	1.00[ASN][1000 genomes]
rs12306645	1.00[ASN][1000 genomes]
rs12310836	0.84[AMR][1000 genomes]
rs12314428	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12316170	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12318633	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12320284	1.00[ASN][1000 genomes]
rs12322319	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28450055	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57108124	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57601151	1.00[ASN][1000 genomes]
rs59250459	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61340540	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580707	1.00[ASN][1000 genomes]
rs6580709	1.00[ASN][1000 genomes]
rs6580710	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580711	1.00[ASN][1000 genomes]
rs6580716	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132684	1.00[ASN][1000 genomes]
rs7139061	1.00[ASN][1000 genomes]
rs7294973	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7295162	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309997	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73295291	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73295300	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73297209	1.00[ASN][1000 genomes]
rs73297210	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73301240	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7342365	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74089066	1.00[ASN][1000 genomes]
rs7955541	1.00[ASN][1000 genomes]
rs7961032	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7962951	1.00[ASN][1000 genomes]
rs7964718	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7969010	1.00[ASN][1000 genomes]
rs7969099	1.00[ASN][1000 genomes]
rs7976165	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][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	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
2	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv899069	chr12:49760499-49924637	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv899070	chr12:49811311-49941500	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49798400-49856000	Weak transcription	Primary T cells from cord blood	blood
2	chr12:49812600-49849000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:49816000-49848800	Weak transcription	Fetal Kidney	kidney
4	chr12:49820400-49854400	Weak transcription	Dnd41	blood
5	chr12:49823000-49854200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:49823000-49856000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:49823000-49915800	Weak transcription	Primary B cells from cord blood	blood
8	chr12:49823200-49856000	Weak transcription	NHEK	skin
9	chr12:49823200-49856400	Weak transcription	HSMM	muscle
10	chr12:49823400-49854400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:49823400-49856000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:49823400-49857400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr12:49823400-49876000	Weak transcription	Osteobl	bone
14	chr12:49828000-49863400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:49829400-49855000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:49831200-49849000	Weak transcription	NH-A	brain
17	chr12:49831600-49852000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:49833000-49849200	Weak transcription	Fetal Intestine Large	intestine
19	chr12:49833000-49849800	Weak transcription	K562	blood
20	chr12:49833400-49848600	Weak transcription	Psoas Muscle	Psoas
21	chr12:49833600-49849800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr12:49833600-49854600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:49834000-49849400	Weak transcription	Left Ventricle	heart
24	chr12:49837600-49856000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:49839200-49876000	Weak transcription	Fetal Thymus	thymus
26	chr12:49840200-49900600	Weak transcription	Pancreas	Pancrea
27	chr12:49840400-49848600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:49840400-49849800	Weak transcription	Aorta	Aorta
29	chr12:49840600-49848200	Weak transcription	A549	lung
30	chr12:49840600-49849200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:49840600-49849600	Weak transcription	Fetal Intestine Small	intestine
32	chr12:49840600-49856000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:49840600-49875800	Weak transcription	Hela-S3	cervix
34	chr12:49840800-49856000	Weak transcription	Fetal Muscle Leg	muscle
35	chr12:49841800-49855800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:49843000-49849600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:49843400-49856000	Weak transcription	Fetal Stomach	stomach
38	chr12:49845600-49856000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr12:49845800-49856800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr12:49846000-49879800	Weak transcription	Fetal Lung	lung
41	chr12:49846200-49849200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:49846200-49855000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:49846400-49854600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:49846400-49854600	Weak transcription	GM12878-XiMat	blood
45	chr12:49846400-49878400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr12:49846800-49856000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr12:49847000-49858200	Weak transcription	Fetal Brain Female	brain
48	chr12:49847400-49848400	Genic enhancers	HepG2	liver
49	chr12:49847400-49855000	Weak transcription	Primary B cells from peripheral blood	blood

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