Variant report

Variant	rs2031128
Chromosome Location	chr10:112589402-112589403
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:112579505..112583802-chr10:112587400..112591373,5	MCF-7	breast:
2	chr10:112587964..112590825-chr10:112590840..112592788,2	K562	blood:

Variant related genes	Relation type
ENSG00000203867	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10885054	0.90[JPT][hapmap]
rs10885055	0.90[JPT][hapmap]
rs12261853	0.90[ASN][1000 genomes]
rs12573386	0.83[CHB][hapmap];0.82[ASN][1000 genomes]
rs3950000	0.92[ASN][1000 genomes]
rs4525160	0.89[ASN][1000 genomes]
rs4918598	0.84[JPT][hapmap]
rs4918599	0.85[JPT][hapmap]
rs4918600	0.85[JPT][hapmap]
rs4918601	0.94[JPT][hapmap]
rs726804	0.85[JPT][hapmap]
rs7922732	0.95[JPT][hapmap];0.86[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	nsv1045608	chr10:112524813-112677557	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1041758	chr10:112552897-112677557	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv467455	chr10:112579299-112612471	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv552172	chr10:112579299-112612471	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv896003	chr10:112579299-112631211	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv896002	chr10:112579299-112638028	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv1051566	chr10:112580049-112730573	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2031128	AFAP1L2	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112572600-112593800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:112577200-112590800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:112577800-112593400	Weak transcription	Thymus	Thymus
4	chr10:112578800-112592400	Weak transcription	Primary T cells from cord blood	blood
5	chr10:112580400-112589800	Enhancers	Colon Smooth Muscle	Colon
6	chr10:112582600-112593000	Weak transcription	K562	blood
7	chr10:112582600-112593400	Weak transcription	Gastric	stomach
8	chr10:112583200-112593400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr10:112583400-112590000	Enhancers	Rectal Smooth Muscle	rectum
10	chr10:112583400-112593800	Weak transcription	Fetal Kidney	kidney
11	chr10:112583400-112594400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr10:112583400-112594800	Weak transcription	Fetal Brain Female	brain
13	chr10:112584400-112592400	Weak transcription	Stomach Mucosa	stomach
14	chr10:112584600-112594000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr10:112584600-112594000	Weak transcription	Small Intestine	intestine
16	chr10:112585600-112593800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr10:112585600-112594200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr10:112586800-112589800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr10:112586800-112590600	Enhancers	Fetal Stomach	stomach
20	chr10:112587200-112589600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr10:112587200-112590200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr10:112587600-112591200	Enhancers	Esophagus	oesophagus
23	chr10:112587800-112592600	Weak transcription	Lung	lung
24	chr10:112587800-112593400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr10:112588000-112590000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr10:112588000-112590800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr10:112588000-112597200	Weak transcription	Adipose Nuclei	Adipose
28	chr10:112588200-112590400	Weak transcription	Pancreas	Pancrea
29	chr10:112588200-112591000	Enhancers	Fetal Thymus	thymus
30	chr10:112588200-112592600	Weak transcription	Psoas Muscle	Psoas
31	chr10:112588200-112593400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr10:112588200-112593600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr10:112588200-112601600	Weak transcription	Brain Anterior Caudate	brain
34	chr10:112588400-112589600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr10:112588400-112590800	Weak transcription	Aorta	Aorta
36	chr10:112588400-112593000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr10:112588400-112593600	Weak transcription	Fetal Lung	lung
38	chr10:112588400-112594000	Weak transcription	Colonic Mucosa	Colon
39	chr10:112588600-112589600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr10:112588600-112589600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr10:112588600-112590400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr10:112588600-112593600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr10:112588600-112594000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr10:112588800-112589600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr10:112588800-112589600	Enhancers	Stomach Smooth Muscle	stomach
46	chr10:112588800-112589800	Enhancers	Right Atrium	heart
47	chr10:112588800-112590600	Enhancers	Fetal Heart	heart
48	chr10:112588800-112591400	Strong transcription	HSMMtube	muscle
49	chr10:112589000-112589600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr10:112589000-112591400	Strong transcription	Fetal Muscle Leg	muscle

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