Variant report

Variant	rs10493253
Chromosome Location	chr1:59373637-59373638
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59242448..59252747-chr1:59356992..59375072,48	K562	blood:
2	chr1:59364854..59367542-chr1:59372083..59374801,2	K562	blood:
3	chr1:59248520..59251420-chr1:59373348..59375708,2	MCF-7	breast:
4	chr1:59366576..59370002-chr1:59372804..59375528,3	K562	blood:
5	chr1:59242448..59251438-chr1:59358057..59375559,39	K562	blood:
6	chr1:59290642..59292329-chr1:59373188..59375440,2	MCF-7	breast:
7	chr1:59370025..59373918-chr1:59374367..59377851,5	K562	blood:

Variant related genes	Relation type
ENSG00000234807	Chromatin interaction
ENSG00000177606	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10789072	0.86[JPT][hapmap]
rs11207321	0.82[JPT][hapmap]
rs11207322	0.81[JPT][hapmap]
rs11207323	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11207325	0.87[CEU][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11207326	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11207332	0.91[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12117564	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12142126	0.85[JPT][hapmap]
rs12404569	0.81[EUR][1000 genomes]
rs12409909	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1536159	0.87[CEU][hapmap];0.87[JPT][hapmap]
rs17118379	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17118404	0.94[YRI][hapmap]
rs17118446	0.93[YRI][hapmap]
rs2057596	0.80[CEU][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes]
rs2953373	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41287666	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6587841	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6658104	0.87[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6661505	0.87[CEU][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6664131	0.87[CEU][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs6681632	0.90[CEU][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6697107	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74078024	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs927743	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005354	chr1:59283572-59535812	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv829959	chr1:59340330-59503085	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv546316	chr1:59368947-59457815	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59369800-59388200	Weak transcription	Gastric	stomach
2	chr1:59370000-59377800	Weak transcription	Aorta	Aorta
3	chr1:59370200-59374000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr1:59370200-59374200	Weak transcription	HSMM	muscle
5	chr1:59370200-59374200	Weak transcription	HSMMtube	muscle
6	chr1:59370200-59374200	Weak transcription	Osteobl	bone
7	chr1:59370200-59374400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:59370200-59374400	Weak transcription	Psoas Muscle	Psoas
9	chr1:59370200-59374400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr1:59370200-59375200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:59370200-59377200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:59370200-59377600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:59370400-59374400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:59370400-59374400	Weak transcription	Adipose Nuclei	Adipose
15	chr1:59370600-59374200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:59370600-59374200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:59370600-59374200	Weak transcription	HMEC	breast
18	chr1:59370600-59374200	Weak transcription	NH-A	brain
19	chr1:59370600-59374200	Weak transcription	NHEK	skin
20	chr1:59370600-59375200	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr1:59370600-59375400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr1:59370600-59375400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:59370600-59377400	Weak transcription	Fetal Muscle Leg	muscle
24	chr1:59370600-59377400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr1:59370800-59374200	Weak transcription	NHLF	lung
26	chr1:59371000-59374200	Weak transcription	Fetal Intestine Large	intestine
27	chr1:59371000-59374200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:59371000-59374400	Weak transcription	Small Intestine	intestine
29	chr1:59371200-59374200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:59371400-59374800	Weak transcription	Stomach Mucosa	stomach
31	chr1:59371600-59374200	Weak transcription	NHDF-Ad	bronchial
32	chr1:59371600-59374400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:59372000-59375400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:59372200-59377400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:59372400-59374400	Weak transcription	Fetal Intestine Small	intestine
36	chr1:59372400-59374400	Weak transcription	A549	lung
37	chr1:59373000-59374000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr1:59373200-59376400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:59373200-59376400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:59373400-59373800	Weak transcription	HUVEC	blood vessel
41	chr1:59373400-59374200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:59373400-59374400	Weak transcription	HepG2	liver
43	chr1:59373400-59374800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr1:59373400-59375200	Enhancers	Hela-S3	cervix
45	chr1:59373400-59377400	Weak transcription	K562	blood
46	chr1:59373400-59378000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:59373600-59376200	Weak transcription	Rectal Mucosa Donor 31	rectum

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