Variant report

Variant	rs969734
Chromosome Location	chr4:87665384-87665385
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10008165	0.87[GIH][hapmap]
rs10016074	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10019950	0.89[ASN][1000 genomes]
rs10023787	0.83[GIH][hapmap]
rs10029671	0.84[CHD][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap]
rs10030525	0.81[ASN][1000 genomes]
rs10031843	0.80[JPT][hapmap]
rs10050311	0.81[CEU][hapmap]
rs1021101	0.84[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs1026861	0.83[GIH][hapmap]
rs1035191	0.95[CHB][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.94[ASN][1000 genomes]
rs10516778	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097115	0.87[GIH][hapmap];0.80[JPT][hapmap]
rs11561681	0.83[AMR][1000 genomes]
rs11930396	0.85[JPT][hapmap];0.80[MEX][hapmap]
rs12331502	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12503659	0.97[ASN][1000 genomes]
rs12510802	0.94[ASN][1000 genomes]
rs13113689	0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1420621	0.89[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1481833	0.84[CHD][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap]
rs17012072	0.86[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17419295	0.80[JPT][hapmap]
rs17419627	1.00[ASW][hapmap];0.91[GIH][hapmap]
rs17419929	0.91[GIH][hapmap];0.80[JPT][hapmap]
rs17420607	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17420966	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17453839	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs17454154	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17454662	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17694112	0.88[CEU][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2006842	0.95[CHB][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.94[ASN][1000 genomes]
rs2054592	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2054593	0.84[CHB][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.89[ASN][1000 genomes]
rs2230600	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2287147	0.88[CEU][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28535527	0.81[ASN][1000 genomes]
rs3775236	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs3775238	0.94[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3775239	0.84[CHB][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[ASN][1000 genomes]
rs4263359	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4693150	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4693152	0.85[JPT][hapmap]
rs4693780	0.94[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4693784	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55640323	0.81[ASN][1000 genomes]
rs55670248	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55978957	0.81[ASN][1000 genomes]
rs57954319	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6531932	0.83[GIH][hapmap]
rs67867077	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72665791	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72665795	0.81[AMR][1000 genomes]
rs7688019	0.85[JPT][hapmap]
rs9307020	0.84[CHD][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap]
rs9307026	0.85[JPT][hapmap]
rs9993042	0.83[GIH][hapmap];0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2757071	chr4:87417291-87689533	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv2759264	chr4:87417291-87689533	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv830001	chr4:87585278-87748643	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv508296	chr4:87636350-87667372	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs969734	LIN54	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87631200-87712200	Weak transcription	Aorta	Aorta
2	chr4:87635200-87737400	Weak transcription	Fetal Brain Male	brain
3	chr4:87636400-87683800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:87639200-87688000	Weak transcription	Fetal Intestine Large	intestine
5	chr4:87639400-87739200	Weak transcription	A549	lung
6	chr4:87641800-87683400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr4:87642200-87692600	Weak transcription	NH-A	brain
8	chr4:87642400-87735800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:87642600-87692400	Weak transcription	Colon Smooth Muscle	Colon
10	chr4:87642600-87697600	Weak transcription	Brain Angular Gyrus	brain
11	chr4:87642600-87719200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr4:87644600-87680600	Weak transcription	NHLF	lung
13	chr4:87650400-87677400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:87651800-87676400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:87652600-87670000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:87655600-87704400	Weak transcription	Hela-S3	cervix
17	chr4:87657200-87665800	Weak transcription	Adipose Nuclei	Adipose
18	chr4:87659000-87676400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:87661600-87665800	Weak transcription	Brain Hippocampus Middle	brain
20	chr4:87661600-87665800	Weak transcription	NHEK	skin
21	chr4:87661600-87671600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr4:87661600-87671600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr4:87661600-87680400	Weak transcription	Brain Substantia Nigra	brain
24	chr4:87661600-87680600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:87661600-87683200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr4:87661600-87710200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr4:87661600-87711400	Weak transcription	Brain Germinal Matrix	brain
28	chr4:87661600-87712000	Weak transcription	Esophagus	oesophagus
29	chr4:87661600-87737800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:87661800-87665800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr4:87661800-87666200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr4:87661800-87670400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr4:87661800-87671400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr4:87661800-87671600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:87661800-87671600	Weak transcription	Lung	lung
36	chr4:87661800-87676600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr4:87661800-87683000	Weak transcription	Fetal Stomach	stomach
38	chr4:87661800-87683200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:87661800-87683800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:87661800-87708000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr4:87661800-87712000	Weak transcription	Fetal Intestine Small	intestine
42	chr4:87661800-87728800	Weak transcription	Pancreas	Pancrea
43	chr4:87662000-87665600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr4:87662000-87665600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr4:87662000-87665800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:87662000-87669000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr4:87662000-87669200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr4:87662000-87675600	Weak transcription	Gastric	stomach
49	chr4:87662400-87669600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:87662600-87665800	Weak transcription	H1 Cell Line	embryonic stem cell

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