Variant report

Variant	rs1021101
Chromosome Location	chr4:87580297-87580298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10008165	0.94[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10023787	0.94[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10029671	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs10030525	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10031843	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1026861	0.94[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1035191	0.81[GIH][hapmap]
rs10516778	0.84[CHD][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11097115	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11943428	0.89[ASN][1000 genomes]
rs11947018	0.83[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1420621	0.91[GIH][hapmap];0.80[JPT][hapmap]
rs1481833	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17011986	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17419295	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17419627	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17419929	0.93[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17420607	0.86[CHD][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs17453839	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17454154	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17694112	0.82[GIH][hapmap]
rs2006842	0.81[GIH][hapmap]
rs2054592	0.80[JPT][hapmap]
rs2230600	0.83[TSI][hapmap]
rs2287147	0.82[GIH][hapmap]
rs28483710	0.89[ASN][1000 genomes]
rs28485273	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28529445	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28534599	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28535527	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28663376	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28678816	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28735881	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3775238	0.81[EUR][1000 genomes]
rs3775239	0.81[GIH][hapmap]
rs4263359	0.81[EUR][1000 genomes]
rs4277747	0.84[ASN][1000 genomes]
rs4513526	0.89[ASN][1000 genomes]
rs4529013	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs4693147	0.94[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap]
rs4693780	0.95[GIH][hapmap];0.80[JPT][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs55640323	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55654230	0.86[ASN][1000 genomes]
rs55746316	0.89[ASN][1000 genomes]
rs55757426	0.89[ASN][1000 genomes]
rs55773619	0.89[ASN][1000 genomes]
rs55879246	0.89[ASN][1000 genomes]
rs55978957	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56150118	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56178389	0.87[ASN][1000 genomes]
rs56296936	0.89[ASN][1000 genomes]
rs56348925	0.87[ASN][1000 genomes]
rs6531932	0.94[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs66669421	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67274037	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67341369	0.84[ASN][1000 genomes]
rs67523832	0.86[ASN][1000 genomes]
rs67867077	0.81[EUR][1000 genomes]
rs67928053	0.89[ASN][1000 genomes]
rs6822396	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs6838659	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs6847139	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs72665759	0.87[ASN][1000 genomes]
rs72665762	0.87[ASN][1000 genomes]
rs72665769	0.86[ASN][1000 genomes]
rs72665771	0.89[ASN][1000 genomes]
rs72665772	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72665777	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7694723	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9307020	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs969734	0.84[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs9993042	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	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
3	nsv1012836	chr4:87279206-87643558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv879522	chr4:87473776-87644842	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv822635	chr4:87479576-87622176	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv879523	chr4:87517609-87594472	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv879524	chr4:87517609-87603929	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	esv2755470	chr4:87536515-87613212	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1021101	FHL2	trans	lymphoblastoid	seeQTL
rs1021101	LIN54	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87571600-87596000	Weak transcription	Pancreas	Pancrea
2	chr4:87574600-87583600	Weak transcription	Ovary	ovary
3	chr4:87574600-87594000	Weak transcription	Fetal Kidney	kidney
4	chr4:87574600-87604400	Weak transcription	Brain Substantia Nigra	brain
5	chr4:87574600-87644400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:87574800-87582000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:87575200-87580800	Weak transcription	Fetal Lung	lung
8	chr4:87575600-87582600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:87575800-87581600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr4:87576000-87582200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:87576200-87593400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:87576400-87581200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr4:87576400-87586000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:87576600-87582200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:87576800-87582400	Weak transcription	A549	lung
16	chr4:87576800-87587800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:87577200-87580600	Weak transcription	Fetal Intestine Large	intestine
18	chr4:87578000-87580400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:87578800-87585800	Weak transcription	Osteobl	bone
20	chr4:87579000-87585800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:87579200-87584400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:87579200-87642600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:87579400-87581400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:87579400-87581600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr4:87579400-87584200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr4:87579400-87587800	Weak transcription	Esophagus	oesophagus
27	chr4:87579400-87591000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:87579400-87593400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:87579400-87594000	Weak transcription	Fetal Stomach	stomach
30	chr4:87579400-87604000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr4:87579400-87644400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:87579600-87581200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:87579600-87581800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:87579600-87584000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:87579600-87584600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr4:87579600-87585800	Weak transcription	HMEC	breast
37	chr4:87579600-87593000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:87579600-87594000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:87579600-87611800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr4:87579800-87587800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:87580200-87580600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links