Variant report

Variant	rs12508205
Chromosome Location	chr4:129243189-129243190
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:129242750..129245400-chr4:129372487..129374943,2	MCF-7	breast:
2	chr4:129230478..129232690-chr4:129242165..129243928,2	MCF-7	breast:
3	chr4:129242863..129244841-chr4:129473916..129475888,2	MCF-7	breast:
4	chr4:129238486..129241419-chr4:129241754..129245055,3	K562	blood:
5	chr4:129236636..129238929-chr4:129241545..129243583,2	MCF-7	breast:
6	chr4:129241239..129245152-chr4:129473526..129476468,3	MCF-7	breast:
7	chr4:129242195..129245805-chr4:129305506..129308663,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273077	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12499030	0.86[AFR][1000 genomes]
rs12645655	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17337491	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975182	1.00[CHB][hapmap]
rs55938082	0.83[AMR][1000 genomes]
rs6534679	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6822446	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12508205	ZSCAN2	trans	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129210200-129245800	Weak transcription	Esophagus	oesophagus
2	chr4:129210400-129246400	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr4:129210400-129247600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr4:129210600-129249800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr4:129211000-129244200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr4:129211000-129246400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr4:129211200-129244000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:129211200-129248200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr4:129211200-129254400	Weak transcription	Brain Substantia Nigra	brain
10	chr4:129221600-129247000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr4:129222200-129264200	Weak transcription	Fetal Thymus	thymus
12	chr4:129223200-129244000	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:129225200-129252200	Weak transcription	Spleen	Spleen
14	chr4:129226600-129244000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:129226800-129244200	Weak transcription	Primary B cells from cord blood	blood
16	chr4:129229000-129243200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr4:129230000-129246600	Weak transcription	Brain Angular Gyrus	brain
18	chr4:129231600-129251200	Weak transcription	Aorta	Aorta
19	chr4:129231800-129243800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:129231800-129245600	Weak transcription	Brain Anterior Caudate	brain
21	chr4:129231800-129251800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:129231800-129252600	Weak transcription	Lung	lung
23	chr4:129231800-129255000	Weak transcription	Left Ventricle	heart
24	chr4:129231800-129261000	Weak transcription	Adipose Nuclei	Adipose
25	chr4:129232200-129244000	Weak transcription	Fetal Muscle Leg	muscle
26	chr4:129232400-129244000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr4:129233000-129247800	Weak transcription	Pancreas	Pancrea
28	chr4:129233600-129245800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr4:129233600-129251600	Weak transcription	Fetal Heart	heart
30	chr4:129234400-129246400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr4:129237400-129244000	Weak transcription	Ovary	ovary
32	chr4:129237600-129244000	Weak transcription	Fetal Intestine Large	intestine
33	chr4:129237600-129245600	Weak transcription	Fetal Intestine Small	intestine
34	chr4:129238600-129244000	Weak transcription	Fetal Brain Female	brain
35	chr4:129239200-129243800	Weak transcription	Primary T cells from cord blood	blood
36	chr4:129240200-129245400	Enhancers	Placenta	Placenta
37	chr4:129241000-129244000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:129241600-129245000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:129241600-129245200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr4:129241600-129249200	Weak transcription	Liver	Liver
41	chr4:129241800-129244800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:129241800-129245200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:129242000-129243800	Enhancers	NH-A	brain
44	chr4:129242000-129245000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:129242000-129245000	Enhancers	Muscle Satellite Cultured Cells	--
46	chr4:129242000-129245000	Enhancers	NHDF-Ad	bronchial
47	chr4:129242000-129245000	Enhancers	Osteobl	bone
48	chr4:129242200-129244000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:129242200-129244800	Enhancers	HSMM	muscle
50	chr4:129242200-129245200	Enhancers	HMEC	breast

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