Variant report

Variant	rs16831068
Chromosome Location	chr2:153272448-153272449
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:153265041..153269898-chr2:153270458..153273464,4	K562	blood:
2	chr2:153271973..153274703-chr2:153276491..153278675,3	MCF-7	breast:
3	chr2:153262402..153264231-chr2:153268942..153273243,3	K562	blood:
4	chr2:153264190..153266541-chr2:153270663..153273065,2	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10497101	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13000076	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13000092	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16831069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16831081	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2164402	1.00[CEU][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2345873	0.81[CHD][hapmap]
rs3811577	0.86[CHD][hapmap]
rs3890370	0.81[CHD][hapmap]
rs4528717	1.00[CEU][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56890291	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv875291	chr2:153251742-153339823	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16831068	GALNT13	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153247400-153277600	Weak transcription	Fetal Intestine Small	intestine
2	chr2:153264200-153288200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:153264400-153274800	Enhancers	Brain Anterior Caudate	brain
4	chr2:153264400-153278000	Weak transcription	Fetal Kidney	kidney
5	chr2:153264600-153277200	Enhancers	A549	lung
6	chr2:153265200-153274800	Weak transcription	Fetal Brain Male	brain
7	chr2:153265200-153278000	Weak transcription	Fetal Lung	lung
8	chr2:153266000-153272800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:153266000-153278800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:153266200-153272600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr2:153266200-153279000	Enhancers	Brain Angular Gyrus	brain
12	chr2:153267000-153277000	Weak transcription	NHLF	lung
13	chr2:153267000-153278800	Enhancers	Brain Cingulate Gyrus	brain
14	chr2:153267000-153279200	Enhancers	Brain Substantia Nigra	brain
15	chr2:153268200-153277400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr2:153268400-153272600	Weak transcription	Fetal Muscle Leg	muscle
17	chr2:153268600-153277000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr2:153268800-153274000	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr2:153269800-153272800	Enhancers	Hela-S3	cervix
20	chr2:153269800-153279200	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr2:153270000-153274800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:153270200-153276200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:153270200-153278000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:153270200-153279800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr2:153270400-153275200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:153270400-153277200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr2:153270400-153277400	Enhancers	Brain Hippocampus Middle	brain
28	chr2:153270400-153277600	Weak transcription	Small Intestine	intestine
29	chr2:153270400-153277800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr2:153270600-153279800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr2:153270800-153272800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr2:153270800-153272800	Enhancers	Pancreas	Pancrea
33	chr2:153270800-153276400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:153271000-153272600	Enhancers	Placenta	Placenta
35	chr2:153271000-153272600	Enhancers	Left Ventricle	heart
36	chr2:153271000-153272600	Enhancers	Ovary	ovary
37	chr2:153271000-153272800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:153271000-153272800	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr2:153271000-153272800	Enhancers	Stomach Mucosa	stomach
40	chr2:153271000-153272800	Genic enhancers	HepG2	liver
41	chr2:153271000-153273800	Enhancers	HMEC	breast
42	chr2:153271000-153274400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr2:153271000-153279000	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr2:153271200-153272600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:153271200-153272600	Enhancers	Aorta	Aorta
46	chr2:153271200-153272800	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr2:153271200-153274200	Enhancers	Psoas Muscle	Psoas
48	chr2:153271400-153272800	Enhancers	HUVEC	blood vessel
49	chr2:153271400-153273000	Enhancers	Muscle Satellite Cultured Cells	--
50	chr2:153271600-153272600	Enhancers	Colon Smooth Muscle	Colon

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