Variant report

Variant	rs56193548
Chromosome Location	chr2:173947052-173947053
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173938088..173944133-chr2:173944779..173953152,16	MCF-7	breast:
2	chr2:173944303..173947485-chr2:173950137..173953589,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091436	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10930579	0.80[ASN][1000 genomes]
rs12615166	0.84[ASN][1000 genomes]
rs12616714	0.82[ASN][1000 genomes]
rs12986917	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12987496	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989116	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12997078	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12998711	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13004212	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017438	0.80[ASN][1000 genomes]
rs13022800	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13029949	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13032010	0.84[ASN][1000 genomes]
rs16861272	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17302977	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2076857	0.85[ASN][1000 genomes]
rs2289397	0.80[ASN][1000 genomes]
rs2289399	0.80[ASN][1000 genomes]
rs34472765	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34681024	0.82[ASN][1000 genomes]
rs34702663	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34862313	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35250703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35599077	0.84[ASN][1000 genomes]
rs36102078	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36103648	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3754741	0.80[ASN][1000 genomes]
rs3754743	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3754744	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3769167	0.80[ASN][1000 genomes]
rs3769187	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3769192	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3769194	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3769199	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3769203	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55913048	0.80[ASN][1000 genomes]
rs56151459	0.84[ASN][1000 genomes]
rs56342397	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6433395	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6741675	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67422536	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71417423	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72905046	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72905080	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[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	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173941600-173947200	Weak transcription	Gastric	stomach
2	chr2:173941600-173955200	Weak transcription	Lung	lung
3	chr2:173941600-173955200	Weak transcription	Pancreas	Pancrea
4	chr2:173941600-173969600	Weak transcription	Spleen	Spleen
5	chr2:173941800-173955200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:173941800-173955200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:173942000-173951400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:173942000-173953000	Weak transcription	Stomach Mucosa	stomach
9	chr2:173942000-173955200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:173942000-173955400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:173942000-173956000	Weak transcription	Fetal Thymus	thymus
12	chr2:173942600-173956400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:173942800-173954800	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr2:173942800-173955800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr2:173942800-173964600	Weak transcription	HUVEC	blood vessel
16	chr2:173942800-173971400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:173943000-173971200	Weak transcription	HSMMtube	muscle
18	chr2:173943200-173955000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:173943400-173951200	Weak transcription	Aorta	Aorta
20	chr2:173943400-173955200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:173943400-173955200	Weak transcription	Dnd41	blood
22	chr2:173943400-173974200	Weak transcription	Fetal Intestine Large	intestine
23	chr2:173943600-173947200	Weak transcription	Right Ventricle	heart
24	chr2:173943800-173956000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:173944000-173947400	Weak transcription	Liver	Liver
26	chr2:173944000-173948600	Weak transcription	Adipose Nuclei	Adipose
27	chr2:173944000-173948600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:173944000-173951200	Weak transcription	Fetal Lung	lung
29	chr2:173944600-173947200	Weak transcription	Left Ventricle	heart
30	chr2:173944600-173947200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr2:173944800-173951200	Weak transcription	Fetal Stomach	stomach
32	chr2:173945000-173947600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:173945200-173947200	Weak transcription	Right Atrium	heart
34	chr2:173945400-173947600	Genic enhancers	A549	lung
35	chr2:173945400-173947800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:173945400-173948400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:173945400-173991200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:173945600-173947800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:173945600-173949400	Weak transcription	NHLF	lung
40	chr2:173945600-173951200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:173945600-173951200	Weak transcription	Hela-S3	cervix
42	chr2:173945800-173947800	Weak transcription	Osteobl	bone
43	chr2:173945800-173951200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:173946000-173947400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:173946000-173947600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:173946000-173947600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:173946000-173947800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:173946200-173947200	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr2:173946200-173947600	Strong transcription	Fetal Muscle Leg	muscle
50	chr2:173946200-173948400	Weak transcription	NHDF-Ad	bronchial

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