Variant report

Variant	rs236335
Chromosome Location	chr1:94064682-94064683
allele	C/T
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	chr1:94059872..94062115-chr1:94064025..94065838,2	K562	blood:
3	chr1:94056848..94059464-chr1:94061387..94064909,3	K562	blood:
4	chr1:94060637..94062992-chr1:94064105..94066678,2	MCF-7	breast:
5	chr1:94048697..94050277-chr1:94063385..94066022,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224093	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs17110063	0.87[TSI][hapmap]
rs17110124	0.89[ASN][1000 genomes]
rs2281474	0.97[ASN][1000 genomes]
rs2295330	0.90[CHB][hapmap]
rs236321	0.91[CEU][hapmap];0.90[CHB][hapmap]
rs236322	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs236323	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs236326	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs236329	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs236330	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs236331	1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs236332	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs236333	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3767973	0.95[ASN][1000 genomes]
rs3767975	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs3767976	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3767977	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]
rs3950119	0.87[TSI][hapmap]
rs57012808	0.97[ASN][1000 genomes]
rs57466479	0.98[ASN][1000 genomes]
rs57914444	0.95[ASN][1000 genomes]
rs59777284	0.95[ASN][1000 genomes]
rs6661488	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.91[ASN][1000 genomes]
rs6671749	0.92[ASN][1000 genomes]
rs6674143	0.90[CHB][hapmap]
rs6677770	0.81[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs6692801	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7516400	0.91[ASN][1000 genomes]
rs7518795	0.94[ASN][1000 genomes]
rs7519939	0.92[ASN][1000 genomes]
rs7524368	0.98[ASN][1000 genomes]
rs7551964	0.92[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
rs236335	BCAR3	cis	parietal	SCAN
rs236335	FNBP1L	cis	cerebellum	SCAN

Chromatin state (count:85 , 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	chr1:94056000-94066000	Weak transcription	Ovary	ovary
3	chr1:94057400-94068000	Genic enhancers	HSMM	muscle
4	chr1:94057400-94069200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:94057400-94071000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:94057600-94106400	Weak transcription	Primary B cells from cord blood	blood
7	chr1:94058000-94066600	Enhancers	Adipose Nuclei	Adipose
8	chr1:94058000-94066600	Enhancers	Fetal Muscle Leg	muscle
9	chr1:94058200-94065000	Enhancers	Colon Smooth Muscle	Colon
10	chr1:94058400-94065200	Enhancers	NHDF-Ad	bronchial
11	chr1:94058400-94068800	Weak transcription	Small Intestine	intestine
12	chr1:94058600-94068000	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr1:94058800-94065600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr1:94059400-94064800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:94059600-94066000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:94059600-94066800	Enhancers	Brain Anterior Caudate	brain
17	chr1:94060200-94065800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:94060200-94065800	Weak transcription	Gastric	stomach
19	chr1:94060200-94066000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:94060200-94066600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:94060200-94078800	Weak transcription	Colonic Mucosa	Colon
22	chr1:94060400-94064800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:94060400-94065400	Strong transcription	Hela-S3	cervix
24	chr1:94060800-94065200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr1:94061200-94065000	Weak transcription	Fetal Intestine Large	intestine
26	chr1:94061200-94078800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:94061400-94066600	Enhancers	Psoas Muscle	Psoas
28	chr1:94061400-94067200	Enhancers	Right Ventricle	heart
29	chr1:94061600-94066200	Weak transcription	Stomach Mucosa	stomach
30	chr1:94061800-94066000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr1:94061800-94066600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:94062000-94065000	Enhancers	Fetal Thymus	thymus
33	chr1:94062000-94067200	Enhancers	Left Ventricle	heart
34	chr1:94062400-94065200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr1:94062400-94066400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:94062400-94066600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:94062400-94066600	Enhancers	Fetal Muscle Trunk	muscle
38	chr1:94062400-94066600	Enhancers	Placenta	Placenta
39	chr1:94062400-94067400	Enhancers	HMEC	breast
40	chr1:94062600-94066600	Strong transcription	Fetal Intestine Small	intestine
41	chr1:94062600-94070000	Weak transcription	Osteobl	bone
42	chr1:94062600-94073000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr1:94062800-94064800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:94062800-94066400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr1:94063000-94065000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:94063000-94065000	Enhancers	Esophagus	oesophagus
47	chr1:94063000-94065000	Enhancers	Rectal Smooth Muscle	rectum
48	chr1:94063000-94065200	Strong transcription	Pancreatic Islets	Pancreatic Islet
49	chr1:94063200-94065000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:94063200-94065000	Enhancers	Fetal Lung	lung

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