Variant report

Variant	rs3767977
Chromosome Location	chr1:94063844-94063845
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94060369..94061952-chr1:94062563..94065175,2	MCF-7	breast:
2	chr1:94056848..94059464-chr1:94061387..94064909,3	K562	blood:
3	chr1:94048697..94050277-chr1:94063385..94066022,2	MCF-7	breast:
4	chr1:94056848..94059524-chr1:94061387..94064381,3	K562	blood:

Variant related genes	Relation type
ENSG00000224093	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs17110124	0.94[ASN][1000 genomes]
rs2281474	0.92[ASN][1000 genomes]
rs2295330	0.90[CHB][hapmap]
rs236321	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs236322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236323	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236326	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236329	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs236330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs236331	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs236332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs236333	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs236335	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3767973	0.91[ASN][1000 genomes]
rs3767975	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs3767976	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57012808	0.92[ASN][1000 genomes]
rs57466479	0.94[ASN][1000 genomes]
rs57914444	0.91[ASN][1000 genomes]
rs59777284	0.91[ASN][1000 genomes]
rs6661488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6671749	0.97[ASN][1000 genomes]
rs6674143	0.90[CHB][hapmap]
rs6692801	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7516400	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7518795	0.98[ASN][1000 genomes]
rs7519939	0.97[ASN][1000 genomes]
rs7524368	0.94[ASN][1000 genomes]
rs7551964	0.97[ASN][1000 genomes]

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	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3767977	BCAR3	cis	parietal	SCAN
rs3767977	EPHX4	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94025600-94073800	Weak transcription	Fetal Brain Female	brain
2	chr1:94048600-94064200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:94056000-94066000	Weak transcription	Ovary	ovary
4	chr1:94057400-94068000	Genic enhancers	HSMM	muscle
5	chr1:94057400-94069200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:94057400-94071000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:94057600-94106400	Weak transcription	Primary B cells from cord blood	blood
8	chr1:94058000-94066600	Enhancers	Adipose Nuclei	Adipose
9	chr1:94058000-94066600	Enhancers	Fetal Muscle Leg	muscle
10	chr1:94058200-94064600	Weak transcription	HUVEC	blood vessel
11	chr1:94058200-94065000	Enhancers	Colon Smooth Muscle	Colon
12	chr1:94058400-94065200	Enhancers	NHDF-Ad	bronchial
13	chr1:94058400-94068800	Weak transcription	Small Intestine	intestine
14	chr1:94058600-94064600	Enhancers	NHLF	lung
15	chr1:94058600-94068000	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr1:94058800-94065600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr1:94059400-94064800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:94059600-94066000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:94059600-94066800	Enhancers	Brain Anterior Caudate	brain
20	chr1:94059800-94064200	Enhancers	Brain Hippocampus Middle	brain
21	chr1:94060200-94064000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:94060200-94064600	Weak transcription	Lung	lung
23	chr1:94060200-94065800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:94060200-94065800	Weak transcription	Gastric	stomach
25	chr1:94060200-94066000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:94060200-94066600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:94060200-94078800	Weak transcription	Colonic Mucosa	Colon
28	chr1:94060400-94064000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:94060400-94064600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:94060400-94064800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:94060400-94065400	Strong transcription	Hela-S3	cervix
32	chr1:94060800-94065200	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr1:94061000-94064200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:94061200-94065000	Weak transcription	Fetal Intestine Large	intestine
35	chr1:94061200-94078800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:94061400-94066600	Enhancers	Psoas Muscle	Psoas
37	chr1:94061400-94067200	Enhancers	Right Ventricle	heart
38	chr1:94061600-94066200	Weak transcription	Stomach Mucosa	stomach
39	chr1:94061800-94064200	Strong transcription	Liver	Liver
40	chr1:94061800-94066000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr1:94061800-94066600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:94062000-94065000	Enhancers	Fetal Thymus	thymus
43	chr1:94062000-94067200	Enhancers	Left Ventricle	heart
44	chr1:94062200-94064000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:94062200-94064200	Weak transcription	NH-A	brain
46	chr1:94062400-94064000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:94062400-94065200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:94062400-94066400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr1:94062400-94066600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:94062400-94066600	Enhancers	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links