Variant report

Variant	rs1346120
Chromosome Location	chr15:57967707-57967708
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57967062..57969940-chr15:57998624..58000773,2	MCF-7	breast:
2	chr15:57965323..57968608-chr15:57997898..58000268,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255529	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11071340	0.80[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.91[AMR][1000 genomes]
rs11071342	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12440250	1.00[CEU][hapmap];0.91[AMR][1000 genomes]
rs12441026	0.85[ASW][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap]
rs1540397	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1540398	0.92[ASN][1000 genomes]
rs1593439	1.00[CEU][hapmap]
rs1690332	1.00[CEU][hapmap]
rs2018558	0.86[ASW][hapmap];0.85[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2081515	0.86[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2098890	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2414516	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2451181	1.00[CEU][hapmap]
rs2453096	1.00[CEU][hapmap]
rs2453097	1.00[CEU][hapmap]
rs2453098	1.00[CEU][hapmap]
rs2554031	0.92[ASN][1000 genomes]
rs2733610	0.92[ASN][1000 genomes]
rs2733611	0.92[ASN][1000 genomes]
rs2733612	0.92[ASN][1000 genomes]
rs28482081	1.00[EUR][1000 genomes]
rs2899603	1.00[CEU][hapmap]
rs2934433	1.00[CEU][hapmap]
rs4564513	1.00[CEU][hapmap]
rs4774279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes]
rs4774280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap]
rs6493941	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6493942	1.00[CEU][hapmap];0.87[GIH][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6493944	0.92[ASN][1000 genomes]
rs7173197	1.00[CEU][hapmap]
rs7181645	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs724785	1.00[CEU][hapmap]
rs8023855	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs8024008	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs9920996	0.91[AMR][1000 genomes]
rs9921015	1.00[CEU][hapmap];0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv530682	chr15:57912502-58108285	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1038667	chr15:57933076-58481870	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv542400	chr15:57933076-58481870	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1346120	DEFA1	trans	brain	seeQTL
rs1346120	IFITM1	trans	brain	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57933400-57982600	Weak transcription	Esophagus	oesophagus
2	chr15:57959600-57982600	Weak transcription	Lung	lung
3	chr15:57959800-57967800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:57960400-57975000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr15:57960800-57985000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr15:57965800-57968200	Enhancers	Stomach Mucosa	stomach
7	chr15:57967000-57968000	Enhancers	Fetal Intestine Small	intestine
8	chr15:57967000-57968400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr15:57967000-57968400	Enhancers	HMEC	breast
10	chr15:57967000-57968600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:57967000-57970800	Enhancers	Placenta Amnion	Placenta Amnion
12	chr15:57967200-57968200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:57967200-57968400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr15:57967200-57974800	Weak transcription	Spleen	Spleen
15	chr15:57967400-57968000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:57967400-57968000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:57967400-57968000	Enhancers	Aorta	Aorta
18	chr15:57967400-57968200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr15:57967400-57968200	Enhancers	Fetal Kidney	kidney
20	chr15:57967400-57968200	Enhancers	Fetal Lung	lung
21	chr15:57967400-57968200	Genic enhancers	Gastric	stomach
22	chr15:57967400-57968200	Strong transcription	Right Ventricle	heart
23	chr15:57967400-57968200	Enhancers	NHEK	skin
24	chr15:57967400-57968400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr15:57967400-57968400	Genic enhancers	Left Ventricle	heart
26	chr15:57967400-57968600	Strong transcription	Adipose Nuclei	Adipose
27	chr15:57967600-57967800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:57967600-57967800	Enhancers	Pancreas	Pancrea
29	chr15:57967600-57968200	Strong transcription	Duodenum Mucosa	Duodenum
30	chr15:57967600-57968400	Enhancers	Fetal Intestine Large	intestine
31	chr15:57967600-57969200	Genic enhancers	Fetal Heart	heart

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