Variant report

Variant	rs3777171
Chromosome Location	chr5:95282971-95282972
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:95282868-95283037	ProgFib	skin:	n/a	n/a
2	POLR2A	chr5:95280186-95283388	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:95276300..95278479-chr5:95281336..95283679,2	MCF-7	breast:
2	chr5:95282858..95287226-chr5:95287357..95291460,4	MCF-7	breast:

Variant related genes	Relation type
ELL2	TF binding region

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10035477	0.81[MEX][hapmap]
rs10052503	1.00[CEU][hapmap];0.91[CHB][hapmap];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10069748	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs10073752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1057963	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs1057964	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs11135442	0.88[MEX][hapmap]
rs11738945	0.87[JPT][hapmap];0.80[EUR][1000 genomes]
rs11741590	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs11742959	0.87[JPT][hapmap];0.80[EUR][1000 genomes]
rs11744881	0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[JPT][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.89[YRI][hapmap]
rs12055262	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1423268	0.83[CHB][hapmap]
rs1423269	0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.80[YRI][hapmap]
rs1458017	0.83[CHB][hapmap]
rs1458018	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs17085231	0.88[MEX][hapmap]
rs17085249	0.91[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap]
rs17085333	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17085428	0.81[JPT][hapmap]
rs1841010	0.83[CHB][hapmap]
rs1862313	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2042340	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs2112566	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2161318	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2270554	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs2348984	0.85[CHB][hapmap]
rs2546199	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2548594	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs3734131	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756703	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777162	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777163	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777164	0.81[EUR][1000 genomes]
rs3777165	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777167	0.84[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs3777168	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777175	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777178	0.87[CEU][hapmap];0.91[CHB][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3777179	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777182	0.85[ASN][1000 genomes]
rs3777183	0.82[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs3777184	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs3777185	0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.93[YRI][hapmap]
rs3777188	0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap]
rs3777189	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs3777190	0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap]
rs3777193	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs3777194	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs3777196	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs3777200	0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap]
rs3777204	0.83[CHB][hapmap]
rs3777207	0.86[TSI][hapmap]
rs3815768	0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap]
rs3822750	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4538631	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4642392	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs55841351	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56002885	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57243277	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57595413	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58921760	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59307279	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6556894	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6556898	0.84[ASN][1000 genomes]
rs6861531	0.88[CEU][hapmap];0.91[CHB][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6877821	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6881355	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6881872	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6883880	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6885567	0.83[CHB][hapmap]
rs6889029	0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap]
rs6894651	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6897997	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6898371	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6898399	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72656689	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7700895	0.88[CEU][hapmap];0.91[CHB][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7705279	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs7705720	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7710422	0.88[ASN][1000 genomes]
rs7724599	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[EUR][1000 genomes]
rs889302	0.83[CHB][hapmap]
rs918629	1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs9314162	0.91[CHB][hapmap];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	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1019566	chr5:95180352-95300677	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	esv2758003	chr5:95231706-95540433	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	esv2759355	chr5:95231706-95540433	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3777171	ELL2	cis	lymphoblastoid	seeQTL
rs3777171	ELL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95260800-95295200	Weak transcription	Primary T cells from cord blood	blood
2	chr5:95262200-95295400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr5:95264800-95285600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr5:95264800-95293800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr5:95265000-95285600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr5:95270000-95283200	Genic enhancers	Muscle Satellite Cultured Cells	--
7	chr5:95270400-95284800	Weak transcription	Fetal Intestine Small	intestine
8	chr5:95270400-95285400	Weak transcription	Right Ventricle	heart
9	chr5:95272400-95283800	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr5:95272600-95283400	Enhancers	Brain Substantia Nigra	brain
11	chr5:95272800-95291200	Weak transcription	NH-A	brain
12	chr5:95273000-95287600	Weak transcription	Primary B cells from cord blood	blood
13	chr5:95273000-95291200	Weak transcription	HSMMtube	muscle
14	chr5:95273800-95285600	Weak transcription	Stomach Mucosa	stomach
15	chr5:95274800-95292200	Weak transcription	Placenta	Placenta
16	chr5:95275400-95291400	Weak transcription	NHDF-Ad	bronchial
17	chr5:95276800-95283000	Enhancers	Brain Anterior Caudate	brain
18	chr5:95277000-95290800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr5:95277200-95283600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:95277200-95284200	Weak transcription	Fetal Heart	heart
21	chr5:95277200-95291600	Weak transcription	Ovary	ovary
22	chr5:95277400-95284200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:95277400-95286400	Enhancers	Brain Cingulate Gyrus	brain
24	chr5:95277600-95283200	Weak transcription	Small Intestine	intestine
25	chr5:95277600-95285600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr5:95277600-95287400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:95277800-95291600	Weak transcription	Fetal Intestine Large	intestine
28	chr5:95278000-95287400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:95278000-95292200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr5:95278400-95286200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:95280400-95283400	Genic enhancers	Liver	Liver
32	chr5:95280400-95284000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:95280600-95283200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr5:95280600-95284000	Enhancers	Brain Hippocampus Middle	brain
35	chr5:95281000-95290800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr5:95281000-95291600	Weak transcription	Aorta	Aorta
37	chr5:95281000-95291600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr5:95281000-95294000	Weak transcription	Esophagus	oesophagus
39	chr5:95281200-95284600	Weak transcription	Brain Angular Gyrus	brain
40	chr5:95281200-95285000	Weak transcription	Osteobl	bone
41	chr5:95281200-95286800	Weak transcription	Psoas Muscle	Psoas
42	chr5:95282000-95283000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr5:95282000-95283400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:95282000-95283400	Enhancers	HUVEC	blood vessel
45	chr5:95282000-95283400	Strong transcription	NHEK	skin
46	chr5:95282000-95284000	Genic enhancers	HSMM	muscle
47	chr5:95282000-95290600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr5:95282200-95283200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr5:95282200-95283800	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr5:95282200-95284000	ZNF genes & repeats	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links