Variant report

Variant	rs3747141
Chromosome Location	chr22:28416547-28416548
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:28416092..28416754-chr22:28837943..28838869,2	K562	blood:
2	chr22:28415721..28416686-chr22:28990407..28991330,6	K562	blood:
3	chr22:28415730..28416730-chr22:28990429..28991381,8	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PITPNB-6	chr22:28416309-28419341	NONHSAT084646

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

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12171034	0.83[ASN][1000 genomes]
rs138638	0.91[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs138650	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs138675	0.82[ASN][1000 genomes]
rs138683	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs138685	0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[TSI][hapmap]
rs1548235	0.82[CHB][hapmap];0.90[CHD][hapmap];0.82[ASN][1000 genomes]
rs2092054	0.87[ASN][1000 genomes]
rs2267121	0.80[TSI][hapmap]
rs4140571	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs470100	0.82[CHB][hapmap]
rs470105	0.86[CHB][hapmap];0.87[CHD][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs6005671	0.83[CHD][hapmap]
rs720621	0.80[CHD][hapmap]
rs7625	0.87[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3747141	ARG2	trans	parietal	SCAN
rs3747141	HPS4	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28396000-28422400	Weak transcription	Primary T cells from cord blood	blood
2	chr22:28397200-28423000	Weak transcription	HepG2	liver
3	chr22:28399400-28425800	Weak transcription	Liver	Liver
4	chr22:28409000-28428000	Genic enhancers	Fetal Muscle Leg	muscle
5	chr22:28409400-28430400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr22:28410200-28423000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr22:28410200-28423400	Weak transcription	Gastric	stomach
8	chr22:28410400-28424200	Weak transcription	Aorta	Aorta
9	chr22:28411000-28423600	Weak transcription	Fetal Intestine Large	intestine
10	chr22:28411800-28418200	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr22:28411800-28418400	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr22:28412000-28418200	Enhancers	Right Ventricle	heart
13	chr22:28412400-28423000	Weak transcription	Adipose Nuclei	Adipose
14	chr22:28414000-28416600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr22:28414200-28417600	Enhancers	Esophagus	oesophagus
16	chr22:28414400-28418600	Genic enhancers	Dnd41	blood
17	chr22:28414600-28417000	Enhancers	Spleen	Spleen
18	chr22:28414800-28417000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr22:28414800-28417400	Enhancers	HSMMtube	muscle
20	chr22:28415000-28417000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr22:28415000-28418600	Enhancers	Fetal Thymus	thymus
22	chr22:28415200-28417800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr22:28415400-28416600	Enhancers	HMEC	breast
24	chr22:28415600-28417400	Enhancers	Brain Germinal Matrix	brain
25	chr22:28415600-28418200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr22:28415600-28418400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr22:28415800-28417200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr22:28415800-28417400	Enhancers	Brain Hippocampus Middle	brain
29	chr22:28415800-28418400	Enhancers	Fetal Brain Male	brain
30	chr22:28415800-28418600	Enhancers	Placenta	Placenta
31	chr22:28416000-28416600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
32	chr22:28416000-28416600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
33	chr22:28416000-28416800	Genic enhancers	Fetal Intestine Small	intestine
34	chr22:28416000-28416800	Enhancers	Pancreas	Pancrea
35	chr22:28416000-28417000	Enhancers	Brain Anterior Caudate	brain
36	chr22:28416000-28417000	Enhancers	Brain Substantia Nigra	brain
37	chr22:28416000-28417200	Enhancers	Stomach Mucosa	stomach
38	chr22:28416000-28417400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr22:28416000-28417600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr22:28416000-28417800	Enhancers	Ovary	ovary
41	chr22:28416000-28418600	Genic enhancers	Fetal Stomach	stomach
42	chr22:28416000-28425000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr22:28416200-28416600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr22:28416200-28416600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr22:28416200-28416600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr22:28416200-28416600	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr22:28416200-28416600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr22:28416200-28416600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr22:28416200-28416600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr22:28416200-28416600	Flanking Active TSS	Colon Smooth Muscle	Colon

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