Variant report

Variant	rs12475594
Chromosome Location	chr2:58433375-58433376
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	chr2:58427142..58430868-chr2:58432407..58434605,4	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11125745	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11889211	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12469873	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17049378	0.86[EUR][1000 genomes]
rs17049429	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2192690	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4395240	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56705143	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56730649	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6725148	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6732505	0.85[ASN][1000 genomes]
rs6735296	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72810360	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72810373	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72812357	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7594702	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999042	chr2:58326123-58530903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv535734	chr2:58326123-58530903	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1007527	chr2:58386271-58477536	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv535735	chr2:58386271-58477536	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv458052	chr2:58388696-58450569	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv582098	chr2:58388696-58450569	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv817995	chr2:58390538-58450569	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58359000-58454000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:58365600-58438000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:58388800-58437400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:58391000-58467000	Weak transcription	HMEC	breast
5	chr2:58396400-58438000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:58396400-58438000	Weak transcription	Pancreas	Pancrea
7	chr2:58397800-58442600	Weak transcription	Brain Anterior Caudate	brain
8	chr2:58398000-58437800	Weak transcription	Primary B cells from cord blood	blood
9	chr2:58399400-58437400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:58400400-58437800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:58403000-58439400	Weak transcription	HSMM	muscle
12	chr2:58403600-58434000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:58403600-58437200	Weak transcription	Fetal Brain Female	brain
14	chr2:58411600-58437400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr2:58413800-58438000	Weak transcription	Thymus	Thymus
16	chr2:58414000-58437600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:58414000-58461400	Weak transcription	NHEK	skin
18	chr2:58414200-58435800	Weak transcription	Fetal Intestine Small	intestine
19	chr2:58414400-58438000	Weak transcription	Esophagus	oesophagus
20	chr2:58414600-58437400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:58414600-58437400	Weak transcription	Brain Germinal Matrix	brain
22	chr2:58415000-58437600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:58415400-58434000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr2:58415800-58437400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:58416000-58437400	Weak transcription	Fetal Kidney	kidney
26	chr2:58416200-58437400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:58416200-58454200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:58416400-58433400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:58416400-58434000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr2:58416400-58437200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:58416400-58438000	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr2:58416600-58467200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:58417800-58439200	Weak transcription	Fetal Brain Male	brain
34	chr2:58421600-58452400	Weak transcription	NH-A	brain
35	chr2:58422000-58434400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr2:58422000-58437400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:58422000-58442800	Weak transcription	Brain Angular Gyrus	brain
38	chr2:58422000-58454200	Weak transcription	Left Ventricle	heart
39	chr2:58423800-58437400	Weak transcription	Primary B cells from peripheral blood	blood
40	chr2:58425000-58442200	Weak transcription	Fetal Heart	heart
41	chr2:58425400-58438400	Weak transcription	Ovary	ovary
42	chr2:58425600-58434200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:58425600-58446600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:58425800-58446600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:58426000-58437200	Weak transcription	GM12878-XiMat	blood
46	chr2:58426000-58437400	Weak transcription	Fetal Muscle Leg	muscle
47	chr2:58426400-58437400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr2:58426400-58438000	Weak transcription	Fetal Intestine Large	intestine
49	chr2:58426600-58436000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr2:58426800-58433800	Weak transcription	H1 Cell Line	embryonic stem cell

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