Variant report

Variant	rs4682418
Chromosome Location	chr3:112350216-112350217
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112350080..112353120-chr3:112708595..112712214,3	K562	blood:
2	chr3:112345807..112347759-chr3:112347769..112350964,3	MCF-7	breast:
3	chr3:112346979..112353983-chr3:112357134..112359925,9	K562	blood:

Variant related genes	Relation type
ENSG00000163607	Chromatin interaction
ENSG00000091986	Chromatin interaction
ENSG00000272844	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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934179	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11712917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1388443	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]
rs16859870	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16859871	0.86[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7349537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7349538	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288955	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833212	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9851689	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861342	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9870432	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9881785	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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
rs4682418	LSAMP	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112331200-112351600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:112331400-112354800	Weak transcription	Psoas Muscle	Psoas
3	chr3:112336200-112351600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:112336600-112351400	Weak transcription	Fetal Lung	lung
5	chr3:112336600-112355800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:112341400-112351400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:112342600-112359600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:112343000-112351600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:112343400-112358000	Weak transcription	Pancreas	Pancrea
10	chr3:112345000-112353800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr3:112345200-112359400	Weak transcription	Esophagus	oesophagus
12	chr3:112346000-112350400	Enhancers	Adipose Nuclei	Adipose
13	chr3:112346200-112352400	Weak transcription	Brain Anterior Caudate	brain
14	chr3:112346200-112352400	Weak transcription	Fetal Brain Female	brain
15	chr3:112346400-112354000	Weak transcription	Fetal Heart	heart
16	chr3:112346600-112353800	Weak transcription	Aorta	Aorta
17	chr3:112347000-112351400	Genic enhancers	Osteobl	bone
18	chr3:112347200-112351200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:112347400-112350600	Weak transcription	Fetal Intestine Large	intestine
20	chr3:112347400-112351600	Weak transcription	Ovary	ovary
21	chr3:112347800-112353200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:112348000-112351400	Enhancers	Colon Smooth Muscle	Colon
23	chr3:112348000-112353200	Enhancers	Rectal Smooth Muscle	rectum
24	chr3:112348200-112351400	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr3:112348200-112351600	Genic enhancers	HSMM	muscle
26	chr3:112348200-112351800	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr3:112348200-112351800	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr3:112348200-112358400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:112348600-112351000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:112348600-112351600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:112348600-112357200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:112348800-112351400	Genic enhancers	Muscle Satellite Cultured Cells	--
33	chr3:112348800-112351600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr3:112348800-112353800	Weak transcription	GM12878-XiMat	blood
35	chr3:112348800-112358400	Weak transcription	Hela-S3	cervix
36	chr3:112349000-112350400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:112349000-112351600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:112349000-112351800	Weak transcription	HMEC	breast
39	chr3:112349000-112351800	Weak transcription	NHEK	skin
40	chr3:112349000-112354400	Enhancers	A549	lung
41	chr3:112349200-112351200	Weak transcription	Fetal Kidney	kidney
42	chr3:112349200-112351400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:112349200-112351400	Weak transcription	Fetal Stomach	stomach
44	chr3:112349200-112352200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr3:112349200-112354400	Weak transcription	Fetal Muscle Leg	muscle
46	chr3:112349400-112350400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr3:112349400-112350800	Weak transcription	HSMMtube	muscle
48	chr3:112349400-112351400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:112349400-112351400	Weak transcription	HUVEC	blood vessel
50	chr3:112349400-112351600	Enhancers	HUES48 Cell Line	embryonic stem cell

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