Variant report

Variant	rs17410154
Chromosome Location	chr1:56047538-56047539
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12127175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4927257	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs904604	0.85[CEU][hapmap]
rs904606	0.85[CEU][hapmap];0.82[JPT][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	nsv10184	chr1:55728755-56084833	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv523489	chr1:56038407-56066503	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17410154	BSND	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56040600-56058600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:56042200-56049600	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:56042200-56052400	Weak transcription	Right Atrium	heart
4	chr1:56043000-56049600	Weak transcription	Brain Germinal Matrix	brain
5	chr1:56043000-56049800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:56043000-56050200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:56043000-56050400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:56044400-56051400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr1:56044600-56048400	Enhancers	HSMM	muscle
10	chr1:56045000-56047600	Enhancers	Osteobl	bone
11	chr1:56045000-56048200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:56045000-56048400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:56045200-56048200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:56045200-56048400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:56045200-56050000	Weak transcription	Ovary	ovary
16	chr1:56045400-56048600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:56045600-56049600	Weak transcription	Fetal Stomach	stomach
18	chr1:56045800-56048400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:56046000-56048000	Enhancers	NHEK	skin
20	chr1:56046000-56048200	Enhancers	NHLF	lung
21	chr1:56046000-56048400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:56046400-56048000	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr1:56046400-56048200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:56046600-56048600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:56047000-56048200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:56047000-56048400	Enhancers	Brain Cingulate Gyrus	brain
27	chr1:56047000-56048400	Enhancers	HMEC	breast
28	chr1:56047000-56048600	Enhancers	NHDF-Ad	bronchial
29	chr1:56047000-56049600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:56047000-56049600	Weak transcription	Fetal Lung	lung
31	chr1:56047000-56050000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:56047000-56050000	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:56047000-56050000	Weak transcription	Colon Smooth Muscle	Colon
34	chr1:56047000-56050200	Weak transcription	Brain Anterior Caudate	brain
35	chr1:56047000-56050400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr1:56047000-56050400	Weak transcription	Brain Substantia Nigra	brain
37	chr1:56047000-56050400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr1:56047000-56050400	Weak transcription	Hela-S3	cervix
39	chr1:56047000-56051400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:56047200-56048000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:56047200-56048200	Enhancers	Aorta	Aorta
42	chr1:56047200-56048200	Enhancers	Psoas Muscle	Psoas
43	chr1:56047200-56048400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:56047200-56049000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:56047400-56047600	Weak transcription	Esophagus	oesophagus
46	chr1:56047400-56048600	Enhancers	Placenta Amnion	Placenta Amnion
47	chr1:56047400-56050400	Weak transcription	NH-A	brain

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