Variant report

Variant	rs3777178
Chromosome Location	chr5:95273915-95273916
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:95273536..95275981-chr5:95297045..95299749,3	K562	blood:
2	chr5:95272618..95275010-chr5:95285327..95286993,2	K562	blood:
3	chr5:95271606..95274908-chr5:95279196..95282633,3	K562	blood:

Variant related genes	Relation type
ENSG00000118985	Chromatin interaction
ENSG00000251314	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10035477	0.83[CEU][hapmap]
rs10052503	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10069748	0.83[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs10073752	0.87[CEU][hapmap];0.91[CHB][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10515232	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[EUR][1000 genomes]
rs1057963	0.91[CHB][hapmap]
rs1057964	0.83[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs11135442	0.83[CEU][hapmap]
rs11738945	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs11741590	0.83[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs11742959	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs11744881	0.83[CEU][hapmap];0.91[CHB][hapmap]
rs12055262	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1423268	0.92[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap]
rs1423269	0.83[CEU][hapmap];0.91[CHB][hapmap]
rs1458017	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs1458018	0.83[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs147295	0.82[YRI][hapmap]
rs17085231	0.83[CEU][hapmap]
rs17085249	0.83[CEU][hapmap];0.91[CHB][hapmap]
rs17085333	0.87[CEU][hapmap];0.91[CHB][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1841010	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs1862313	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2042340	0.91[CHB][hapmap]
rs2112566	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2161318	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2270554	0.83[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2348984	0.95[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap]
rs2546199	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2548594	0.83[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs3734131	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3756703	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777162	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777163	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777165	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3777166	0.88[CEU][hapmap];0.91[CHB][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3777167	0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3777168	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3777171	0.87[CEU][hapmap];0.91[CHB][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3777173	0.87[CEU][hapmap];0.91[CHB][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3777175	0.87[CEU][hapmap];0.91[CHB][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3777179	1.00[CEU][hapmap];0.91[CHB][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777183	0.83[CHB][hapmap]
rs3777184	0.91[CHB][hapmap]
rs3777185	0.83[CEU][hapmap];0.91[CHB][hapmap]
rs3777188	0.83[CEU][hapmap];0.91[CHB][hapmap]
rs3777189	0.91[CHB][hapmap]
rs3777190	0.83[CEU][hapmap];0.91[CHB][hapmap]
rs3777193	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs3777194	0.83[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs3777196	0.83[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs3777200	0.83[CEU][hapmap];0.91[CHB][hapmap]
rs3777204	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs3815768	0.83[CEU][hapmap];0.91[CHB][hapmap]
rs3822750	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4538631	0.82[CHB][hapmap]
rs4563648	0.83[ASN][1000 genomes]
rs4642392	0.83[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs55841351	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56002885	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57243277	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57595413	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58921760	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59307279	0.96[EUR][1000 genomes]
rs6556894	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6861531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6877821	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6879652	0.83[YRI][hapmap]
rs6881355	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6881872	0.87[CEU][hapmap];0.91[CHB][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6883880	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6885567	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs6889029	0.83[CEU][hapmap];0.91[CHB][hapmap]
rs6894651	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6897997	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6898371	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6898399	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72656689	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7700895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7705279	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7705720	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7716691	0.80[CEU][hapmap]
rs7724599	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs889302	0.92[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs918629	0.93[YRI][hapmap]
rs9314162	0.91[CHB][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3777178	ELL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95236400-95276600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:95238200-95282000	Weak transcription	HUVEC	blood vessel
3	chr5:95243400-95278800	Weak transcription	Lung	lung
4	chr5:95243600-95274200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr5:95257400-95276600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:95259400-95274600	Weak transcription	Psoas Muscle	Psoas
7	chr5:95260000-95280600	Weak transcription	Esophagus	oesophagus
8	chr5:95260800-95295200	Weak transcription	Primary T cells from cord blood	blood
9	chr5:95262200-95295400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr5:95263800-95278400	Weak transcription	Colonic Mucosa	Colon
11	chr5:95264800-95275200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr5:95264800-95276000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:95264800-95279800	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr5:95264800-95285600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr5:95264800-95293800	Weak transcription	Primary B cells from peripheral blood	blood
16	chr5:95265000-95285600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr5:95265400-95281800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr5:95266600-95274400	Weak transcription	NHLF	lung
19	chr5:95267000-95277000	Weak transcription	Fetal Thymus	thymus
20	chr5:95267200-95280200	Weak transcription	Aorta	Aorta
21	chr5:95267400-95280000	Weak transcription	A549	lung
22	chr5:95267600-95274800	Weak transcription	NHDF-Ad	bronchial
23	chr5:95268400-95274600	Weak transcription	Brain Anterior Caudate	brain
24	chr5:95269800-95275000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr5:95270000-95274200	Genic enhancers	Osteobl	bone
26	chr5:95270000-95283200	Genic enhancers	Muscle Satellite Cultured Cells	--
27	chr5:95270400-95276600	Weak transcription	Ovary	ovary
28	chr5:95270400-95276600	Weak transcription	Small Intestine	intestine
29	chr5:95270400-95277000	Weak transcription	Fetal Intestine Large	intestine
30	chr5:95270400-95277400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr5:95270400-95284800	Weak transcription	Fetal Intestine Small	intestine
32	chr5:95270400-95285400	Weak transcription	Right Ventricle	heart
33	chr5:95270600-95276600	Weak transcription	Fetal Heart	heart
34	chr5:95270800-95279200	Genic enhancers	HepG2	liver
35	chr5:95271200-95274800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:95271400-95275400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr5:95271400-95278800	Genic enhancers	NHEK	skin
38	chr5:95271600-95274000	Enhancers	Brain Cingulate Gyrus	brain
39	chr5:95271600-95274800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr5:95271600-95276200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr5:95271600-95276200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr5:95272000-95276200	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr5:95272200-95277800	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr5:95272200-95278800	Enhancers	Brain Angular Gyrus	brain
45	chr5:95272400-95276600	Weak transcription	Adipose Nuclei	Adipose
46	chr5:95272400-95278800	Enhancers	Brain Hippocampus Middle	brain
47	chr5:95272400-95283800	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr5:95272600-95276800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr5:95272600-95283400	Enhancers	Brain Substantia Nigra	brain
50	chr5:95272800-95274400	Genic enhancers	Left Ventricle	heart

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