Variant report

Variant	rs1388443
Chromosome Location	chr3:112353331-112353332
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112338141..112343361-chr3:112351475..112354709,4	MCF-7	breast:
2	chr3:112333133..112335338-chr3:112353119..112355694,2	MCF-7	breast:
3	chr3:112346448..112348470-chr3:112351397..112354527,3	K562	blood:
4	chr3:112346979..112353983-chr3:112357134..112359925,9	K562	blood:

Variant related genes	Relation type
ENSG00000091986	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10934178	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10934179	0.83[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11712917	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16859870	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16859871	0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682418	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7349537	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7349538	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9288955	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9833212	0.83[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9851689	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9861342	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9870432	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9881785	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1388443	LSAMP	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112331400-112354800	Weak transcription	Psoas Muscle	Psoas
2	chr3:112336600-112355800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:112342600-112359600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:112343400-112358000	Weak transcription	Pancreas	Pancrea
5	chr3:112345000-112353800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr3:112345200-112359400	Weak transcription	Esophagus	oesophagus
7	chr3:112346400-112354000	Weak transcription	Fetal Heart	heart
8	chr3:112346600-112353800	Weak transcription	Aorta	Aorta
9	chr3:112348200-112358400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:112348600-112357200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:112348800-112353800	Weak transcription	GM12878-XiMat	blood
12	chr3:112348800-112358400	Weak transcription	Hela-S3	cervix
13	chr3:112349000-112354400	Enhancers	A549	lung
14	chr3:112349200-112354400	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:112350000-112353600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:112350000-112354400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:112350000-112354600	Enhancers	H1 Cell Line	embryonic stem cell
18	chr3:112350000-112354600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr3:112350000-112354600	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr3:112350200-112354400	Flanking Active TSS	NHDF-Ad	bronchial
21	chr3:112351200-112353800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:112351200-112354000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:112351200-112355600	Enhancers	Fetal Kidney	kidney
24	chr3:112351400-112354000	Enhancers	Fetal Lung	lung
25	chr3:112351400-112354200	Enhancers	Fetal Stomach	stomach
26	chr3:112351400-112355000	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr3:112351400-112358600	Transcr. at gene 5' and 3'	Osteobl	bone
28	chr3:112351600-112353400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:112351600-112354200	Enhancers	H9 Cell Line	embryonic stem cell
30	chr3:112351800-112354000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr3:112351800-112354200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:112351800-112354800	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr3:112351800-112355200	Weak transcription	Right Atrium	heart
34	chr3:112351800-112357800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:112352000-112353600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:112352000-112356000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:112352200-112354000	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr3:112352200-112354400	Enhancers	Placenta Amnion	Placenta Amnion
39	chr3:112352400-112353600	Genic enhancers	HSMM	muscle
40	chr3:112352400-112353800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:112352400-112354400	Flanking Active TSS	Colon Smooth Muscle	Colon
42	chr3:112352600-112353400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr3:112352600-112353600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:112352600-112353800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:112352600-112353800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:112352600-112354000	Weak transcription	HMEC	breast
47	chr3:112352600-112355000	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr3:112352600-112358400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:112352800-112353800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:112352800-112353800	Weak transcription	Fetal Brain Female	brain

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