Variant report

Variant	rs293847
Chromosome Location	chr3:191114590-191114591
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:191113983..191115834-chr3:191118918..191120491,2	K562	blood:
2	chr3:191109601..191112408-chr3:191114470..191116944,2	K562	blood:
3	chr3:191114086..191115834-chr3:191118991..191121989,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PYDC2-5	chr3:191113180-191116458	NONHSAT093967

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1066867	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12636442	0.84[ASN][1000 genomes]
rs12636482	0.84[ASN][1000 genomes]
rs167150	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16866491	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs169860	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs176824	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs188450	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2018996	0.81[ASN][1000 genomes]
rs293799	0.93[CHB][hapmap];0.84[ASN][1000 genomes]
rs293843	0.82[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs293845	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs293855	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs293860	0.86[AMR][1000 genomes]
rs297370	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs366693	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3796222	0.81[ASN][1000 genomes]
rs485788	0.82[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs492470	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs510014	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs523100	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56772293	0.84[ASN][1000 genomes]
rs574206	0.82[CEU][hapmap];0.94[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs579405	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58266557	0.83[ASN][1000 genomes]
rs61177977	0.82[ASN][1000 genomes]
rs695879	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73888563	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191079400-191115800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:191079600-191116400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:191079600-191121200	Weak transcription	Gastric	stomach
4	chr3:191080200-191118800	Weak transcription	Pancreas	Pancrea
5	chr3:191087000-191115400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:191088600-191119600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:191093400-191119400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:191093400-191121400	Weak transcription	Esophagus	oesophagus
9	chr3:191094800-191114800	Weak transcription	A549	lung
10	chr3:191096000-191130200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:191096600-191114800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:191099400-191122000	Weak transcription	Fetal Brain Male	brain
13	chr3:191099600-191114600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr3:191099600-191120000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:191099800-191117600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:191100200-191119200	Weak transcription	Right Ventricle	heart
17	chr3:191100200-191119400	Weak transcription	Psoas Muscle	Psoas
18	chr3:191100200-191119600	Weak transcription	K562	blood
19	chr3:191100400-191117400	Weak transcription	Fetal Stomach	stomach
20	chr3:191100400-191117400	Weak transcription	Lung	lung
21	chr3:191100400-191117800	Weak transcription	Small Intestine	intestine
22	chr3:191100400-191120000	Weak transcription	Spleen	Spleen
23	chr3:191100400-191121600	Weak transcription	Fetal Brain Female	brain
24	chr3:191100800-191115400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:191101000-191115600	Weak transcription	Fetal Kidney	kidney
26	chr3:191101000-191117600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:191101200-191115200	Weak transcription	Fetal Heart	heart
28	chr3:191101200-191115600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr3:191101200-191115800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr3:191101200-191117000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr3:191102200-191117600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:191103200-191119400	Weak transcription	HSMMtube	muscle
33	chr3:191104800-191116600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:191106800-191117200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:191107200-191114600	Strong transcription	HUVEC	blood vessel
36	chr3:191107400-191117200	Weak transcription	HepG2	liver
37	chr3:191108000-191117400	Weak transcription	NHEK	skin
38	chr3:191108600-191118000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr3:191108600-191118800	Weak transcription	Brain Germinal Matrix	brain
40	chr3:191108800-191115600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr3:191108800-191115600	Weak transcription	Ovary	ovary
42	chr3:191108800-191119400	Weak transcription	Aorta	Aorta
43	chr3:191109200-191117600	Weak transcription	Fetal Muscle Leg	muscle
44	chr3:191109600-191116400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:191110400-191115600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:191110400-191118000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr3:191110600-191115400	Weak transcription	Colon Smooth Muscle	Colon
48	chr3:191110600-191117600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:191110600-191117600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr3:191110800-191119400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links