Variant report

Variant	rs16831013
Chromosome Location	chr2:153233059-153233060
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:153231246..153233171-chr2:153235303..153238284,3	MCF-7	breast:
2	chr2:153232621..153235253-chr2:153237551..153240252,2	K562	blood:
3	chr2:153215582..153217923-chr2:153232272..153234724,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10432492	0.81[JPT][hapmap]
rs11695776	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12468749	0.87[CHB][hapmap]
rs12478426	0.81[JPT][hapmap]
rs12987825	0.95[MEX][hapmap];0.82[TSI][hapmap]
rs13405341	0.87[JPT][hapmap]
rs16831028	0.81[JPT][hapmap]
rs35589152	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4293523	0.87[CHB][hapmap]
rs4544376	1.00[ASW][hapmap];0.88[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4664106	0.87[JPT][hapmap]
rs7593505	0.87[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	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1005012	chr2:153206764-153273886	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16831013	GALNT13	cis	cerebellum	SCAN
rs16831013	CACNB4	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153206800-153240800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:153207600-153246400	Weak transcription	Fetal Intestine Small	intestine
3	chr2:153209400-153237000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:153216600-153233400	Weak transcription	Fetal Lung	lung
5	chr2:153223400-153237000	Weak transcription	Right Atrium	heart
6	chr2:153224200-153234600	Weak transcription	Adipose Nuclei	Adipose
7	chr2:153224800-153246000	Weak transcription	Fetal Stomach	stomach
8	chr2:153226200-153233200	Weak transcription	Hela-S3	cervix
9	chr2:153226200-153237000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:153226200-153237000	Weak transcription	Aorta	Aorta
11	chr2:153226200-153237000	Weak transcription	Left Ventricle	heart
12	chr2:153226200-153249400	Weak transcription	Right Ventricle	heart
13	chr2:153226200-153251800	Weak transcription	HSMMtube	muscle
14	chr2:153226800-153236600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr2:153226800-153237000	Weak transcription	NHLF	lung
16	chr2:153226800-153240000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:153227000-153237200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr2:153227000-153242000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:153227800-153239400	Weak transcription	NHDF-Ad	bronchial
20	chr2:153228000-153236600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:153228800-153234200	Enhancers	Brain Anterior Caudate	brain
22	chr2:153229200-153236600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:153229200-153252400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:153229400-153233400	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:153229600-153237000	Weak transcription	Fetal Kidney	kidney
26	chr2:153231400-153237000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr2:153232000-153236800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:153232000-153237400	Enhancers	HepG2	liver
29	chr2:153232200-153237000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:153232600-153233200	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr2:153232600-153233600	Enhancers	Psoas Muscle	Psoas
32	chr2:153232600-153233800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:153232600-153233800	Enhancers	NHEK	skin
34	chr2:153232600-153239400	Enhancers	Brain Substantia Nigra	brain
35	chr2:153232800-153233200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr2:153232800-153233200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr2:153232800-153233200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr2:153232800-153233200	Enhancers	Fetal Muscle Leg	muscle
39	chr2:153232800-153233600	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr2:153232800-153233600	Enhancers	Brain Hippocampus Middle	brain
41	chr2:153232800-153233600	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr2:153232800-153233600	Enhancers	Stomach Mucosa	stomach
43	chr2:153232800-153233800	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr2:153232800-153233800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:153232800-153233800	Enhancers	Placenta	Placenta
46	chr2:153232800-153233800	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr2:153232800-153233800	Enhancers	HMEC	breast
48	chr2:153232800-153235200	Enhancers	A549	lung
49	chr2:153233000-153233400	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr2:153233000-153233400	Enhancers	Gastric	stomach

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