Variant report

Variant	rs1386478
Chromosome Location	chr3:113680951-113680952
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:113680868..113682791-chr3:113775643..113777520,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151576	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11926807	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap]
rs13064372	0.91[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.82[YRI][hapmap]
rs13064466	0.91[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs13069900	0.91[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs13071100	0.91[CEU][hapmap]
rs13086657	0.91[CEU][hapmap]
rs13087347	0.91[CEU][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs13096290	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1487265	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2029228	0.82[YRI][hapmap]
rs2134655	1.00[YRI][hapmap]
rs2242316	1.00[ASW][hapmap];0.91[CEU][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs2632241	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];0.87[TSI][hapmap]
rs324553	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.85[TSI][hapmap]
rs324555	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];0.80[TSI][hapmap]
rs324556	0.87[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap]
rs7631864	0.91[CEU][hapmap];0.82[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Crohn's disease and psoriasis	22482804	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1386478	KIAA1407	cis	lymphoblastoid	seeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113667600-113695800	Weak transcription	Left Ventricle	heart
2	chr3:113667800-113683000	Weak transcription	Small Intestine	intestine
3	chr3:113667800-113683400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:113667800-113685000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:113667800-113685200	Weak transcription	A549	lung
6	chr3:113667800-113696800	Weak transcription	Right Ventricle	heart
7	chr3:113667800-113710800	Weak transcription	Esophagus	oesophagus
8	chr3:113668000-113687800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:113668000-113692000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:113668000-113699000	Weak transcription	Stomach Mucosa	stomach
11	chr3:113668200-113696200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:113668400-113724200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:113670200-113681400	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:113670600-113681200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:113672000-113685600	Strong transcription	Primary B cells from cord blood	blood
16	chr3:113672400-113698000	Weak transcription	Ovary	ovary
17	chr3:113673000-113700800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr3:113673200-113682000	Weak transcription	Dnd41	blood
19	chr3:113673200-113683400	Weak transcription	Fetal Thymus	thymus
20	chr3:113673200-113683400	Weak transcription	Lung	lung
21	chr3:113673200-113685200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:113673200-113688600	Weak transcription	Spleen	Spleen
23	chr3:113673400-113683000	Weak transcription	Primary T cells from cord blood	blood
24	chr3:113673400-113687600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:113673400-113696400	Weak transcription	Brain Angular Gyrus	brain
26	chr3:113673400-113704400	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:113673400-113761000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:113674000-113743800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:113674200-113685800	Weak transcription	Brain Anterior Caudate	brain
30	chr3:113674800-113682200	Strong transcription	Primary B cells from peripheral blood	blood
31	chr3:113675600-113681400	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr3:113676200-113682200	Strong transcription	Fetal Intestine Large	intestine
33	chr3:113676400-113723400	Weak transcription	Brain Substantia Nigra	brain
34	chr3:113677000-113685600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr3:113677600-113681000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr3:113677600-113682400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:113677600-113685000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:113677800-113681000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr3:113678000-113681000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr3:113678000-113681600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr3:113678000-113681800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:113678000-113687400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:113678000-113693200	Weak transcription	Fetal Intestine Small	intestine
44	chr3:113678000-113693200	Weak transcription	Fetal Stomach	stomach
45	chr3:113678000-113724400	Weak transcription	Pancreas	Pancrea
46	chr3:113678000-113731400	Weak transcription	Gastric	stomach
47	chr3:113678600-113681400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:113678800-113686600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:113679200-113681000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr3:113679200-113688200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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