Variant report

Variant	rs3811575
Chromosome Location	chr2:153282883-153282884
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:153276442..153278166-chr2:153280321..153283147,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10184210	0.90[JPT][hapmap]
rs11898429	0.89[GIH][hapmap];0.90[JPT][hapmap]
rs12614465	0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs16831066	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16831125	0.82[JPT][hapmap]
rs2346201	0.81[JPT][hapmap]
rs2346202	0.90[JPT][hapmap]
rs3901192	0.90[JPT][hapmap]
rs4371310	0.86[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4664579	0.81[JPT][hapmap]
rs4664583	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59348655	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6434028	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6721741	0.94[JPT][hapmap]
rs6724305	0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs6729611	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6736856	0.95[JPT][hapmap]
rs7586834	0.81[CHD][hapmap]
rs7600624	0.81[CHD][hapmap]
rs7607429	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9677373	0.81[JPT][hapmap]

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	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
3	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
4	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3811575	GALNT13	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153264200-153288200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:153272600-153284800	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:153272600-153285400	Weak transcription	Gastric	stomach
4	chr2:153272800-153288200	Weak transcription	Right Atrium	heart
5	chr2:153278200-153287400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:153278400-153283000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:153278400-153286000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:153278400-153289800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:153278600-153284200	Weak transcription	Fetal Lung	lung
10	chr2:153278600-153288000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:153278800-153288200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:153278800-153290600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:153278800-153291200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:153279000-153284600	Weak transcription	Stomach Mucosa	stomach
15	chr2:153279000-153287400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:153279000-153287600	Weak transcription	Adipose Nuclei	Adipose
17	chr2:153279200-153283000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr2:153279200-153288200	Weak transcription	Left Ventricle	heart
19	chr2:153279400-153285400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:153279400-153288200	Weak transcription	Placenta	Placenta
21	chr2:153279400-153288200	Weak transcription	Lung	lung
22	chr2:153280000-153305200	Enhancers	Brain Cingulate Gyrus	brain
23	chr2:153280200-153283400	Weak transcription	HMEC	breast
24	chr2:153280200-153284400	Weak transcription	Hela-S3	cervix
25	chr2:153280400-153287600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:153280600-153284400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:153280600-153286400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:153280600-153287400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:153280800-153286400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:153280800-153288400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr2:153281200-153285400	Weak transcription	Psoas Muscle	Psoas
32	chr2:153281400-153283800	Enhancers	Brain Angular Gyrus	brain
33	chr2:153281400-153285800	Enhancers	Brain Hippocampus Middle	brain
34	chr2:153281400-153285800	Enhancers	Brain Substantia Nigra	brain
35	chr2:153281600-153285400	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr2:153281600-153291600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:153282000-153283400	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr2:153282200-153283000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:153282200-153283000	Enhancers	NHDF-Ad	bronchial
40	chr2:153282200-153283200	Enhancers	H9 Cell Line	embryonic stem cell
41	chr2:153282200-153283400	Enhancers	Fetal Kidney	kidney
42	chr2:153282200-153283600	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr2:153282200-153283600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:153282200-153283600	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr2:153282200-153283600	Enhancers	Ovary	ovary
46	chr2:153282200-153283600	Enhancers	HSMMtube	muscle
47	chr2:153282200-153283800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr2:153282200-153285000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:153282400-153283000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:153282400-153283000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links