Variant report

Variant	rs1077884
Chromosome Location	chr1:114636635-114636636
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114635981..114636840-chr1:114825182..114826118,4	MCF-7	breast:
2	chr1:114635004..114637775-chr1:114660348..114663171,3	MCF-7	breast:
3	chr1:114635280..114637076-chr16:67188137..67191058,2	MCF-7	breast:
4	chr1:114636244..114636762-chr1:114828230..114828909,2	MCF-7	breast:
5	chr1:114636043..114636656-chr1:114888987..114889518,2	MCF-7	breast:
6	chr1:114636107..114636908-chr1:114825158..114826472,6	MCF-7	breast:
7	chr1:114635427..114637656-chr1:114664752..114666679,2	MCF-7	breast:
8	chr1:114635964..114636990-chr1:114757973..114758697,4	MCF-7	breast:
9	chr1:114521456..114522097-chr1:114635919..114636683,3	MCF-7	breast:
10	chr1:114635498..114636793-chr1:114761766..114763145,4	MCF-7	breast:
11	chr1:114635940..114636836-chr1:114889119..114889768,3	MCF-7	breast:
12	chr1:114636253..114637885-chr1:114697898..114700457,2	MCF-7	breast:
13	chr1:114634509..114637387-chr1:114642285..114643909,2	K562	blood:
14	chr1:114631687..114633246-chr1:114634431..114636796,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000116774	Chromatin interaction
ENSG00000102871	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10494166	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1053135	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1079093	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10858032	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11102729	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12566797	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs2279380	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs745392	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv1849780	chr1:114577463-114663164	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1077884	WDR77	cis	cerebellum	SCAN
rs1077884	DENND2C	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114619200-114640200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:114625400-114639600	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr1:114625400-114639800	Weak transcription	Right Atrium	heart
4	chr1:114630400-114675800	Weak transcription	Pancreas	Pancrea
5	chr1:114631400-114638400	Enhancers	Fetal Lung	lung
6	chr1:114631400-114638800	Weak transcription	Fetal Brain Female	brain
7	chr1:114631800-114636800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:114632200-114661000	Weak transcription	Brain Germinal Matrix	brain
9	chr1:114632400-114637000	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:114633000-114637600	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr1:114633000-114648000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:114634200-114648400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:114634600-114637800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
14	chr1:114634800-114639600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:114635600-114636800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:114635600-114636800	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:114635800-114639000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:114636000-114637400	Enhancers	NHEK	skin
19	chr1:114636000-114637600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:114636000-114637600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:114636000-114637600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:114636000-114637600	Enhancers	NH-A	brain
23	chr1:114636000-114637800	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr1:114636000-114637800	Enhancers	HMEC	breast
25	chr1:114636000-114637800	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr1:114636000-114638200	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr1:114636200-114636800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:114636200-114637000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:114636200-114637000	Bivalent Enhancer	NHDF-Ad	bronchial
30	chr1:114636200-114637200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:114636200-114637200	Enhancers	Left Ventricle	heart
32	chr1:114636200-114637400	Enhancers	HSMM	muscle
33	chr1:114636200-114638200	Genic enhancers	H9 Cell Line	embryonic stem cell
34	chr1:114636400-114637000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:114636400-114639800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:114636600-114636800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr1:114636600-114636800	Enhancers	Fetal Heart	heart
38	chr1:114636600-114637000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:114636600-114637000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr1:114636600-114637000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:114636600-114637000	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr1:114636600-114637200	Enhancers	Osteobl	bone
43	chr1:114636600-114637400	Enhancers	Muscle Satellite Cultured Cells	--
44	chr1:114636600-114637400	Enhancers	HSMMtube	muscle
45	chr1:114636600-114637600	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr1:114636600-114637600	Enhancers	Rectal Smooth Muscle	rectum
47	chr1:114636600-114637800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:114636600-114637800	Enhancers	Fetal Stomach	stomach
49	chr1:114636600-114638200	Genic enhancers	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links