Variant report

Variant	rs9833212
Chromosome Location	chr3:112342113-112342114
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112342080..112344634-chr3:112358848..112360765,3	MCF-7	breast:
2	chr3:112338141..112343361-chr3:112351475..112354709,4	MCF-7	breast:
3	chr3:112340519..112345126-chr3:112357206..112361448,6	MCF-7	breast:
4	chr3:112340785..112342316-chr3:112345669..112347185,2	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	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10934179	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11712917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1388443	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]
rs16859870	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16859871	0.86[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682418	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]
rs7349537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7349538	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9288955	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	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9861342	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9870432	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881785	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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
rs9833212	LSAMP	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112312600-112346200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:112312600-112347200	Weak transcription	Fetal Intestine Large	intestine
3	chr3:112316200-112342800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:112330400-112346800	Strong transcription	NHLF	lung
5	chr3:112331200-112351600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:112331400-112354800	Weak transcription	Psoas Muscle	Psoas
7	chr3:112335200-112342200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:112335200-112345400	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:112336200-112347400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:112336200-112351600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:112336400-112346800	Weak transcription	Fetal Stomach	stomach
12	chr3:112336600-112351400	Weak transcription	Fetal Lung	lung
13	chr3:112336600-112355800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:112337000-112346800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:112338000-112349400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:112338400-112346200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:112338600-112342200	Weak transcription	HUVEC	blood vessel
18	chr3:112338800-112343600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:112340000-112342200	Enhancers	Ovary	ovary
20	chr3:112340000-112342600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:112340000-112342800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:112340000-112343400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:112340200-112342600	Strong transcription	Stomach Smooth Muscle	stomach
24	chr3:112340200-112342800	Strong transcription	HSMMtube	muscle
25	chr3:112340800-112348200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:112341000-112342600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:112341000-112346200	Weak transcription	Aorta	Aorta
28	chr3:112341000-112348400	Weak transcription	Fetal Kidney	kidney
29	chr3:112341200-112342200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:112341200-112343400	Enhancers	Hela-S3	cervix
31	chr3:112341200-112344000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:112341400-112342200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:112341400-112342200	Weak transcription	Adipose Nuclei	Adipose
34	chr3:112341400-112344200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:112341400-112351400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:112341800-112342400	Enhancers	Colon Smooth Muscle	Colon
37	chr3:112341800-112342400	Genic enhancers	HSMM	muscle
38	chr3:112341800-112342400	Enhancers	K562	blood
39	chr3:112341800-112342800	Enhancers	H9 Cell Line	embryonic stem cell
40	chr3:112341800-112343200	Enhancers	HMEC	breast
41	chr3:112341800-112343400	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr3:112341800-112343600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:112341800-112344200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:112341800-112345200	Genic enhancers	Osteobl	bone
45	chr3:112341800-112347800	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr3:112341800-112348000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:112341800-112348200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:112342000-112342600	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr3:112342000-112342800	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr3:112342000-112342800	Genic enhancers	A549	lung

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