Variant report

Variant	rs10934179
Chromosome Location	chr3:112348632-112348633
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112345807..112347759-chr3:112347769..112350964,3	MCF-7	breast:
2	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	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11712917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16859870	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16859871	0.86[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[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];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7349537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7349538	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9833212	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]
rs9851689	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9861342	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.91[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];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9881785	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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
rs10934179	LSAMP	cis	parietal	SCAN

Chromatin state (count:66 , 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	chr3:112338000-112349400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:112341400-112351400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:112342600-112350000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:112342600-112359600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:112342800-112350000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:112343000-112349600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:112343000-112351600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:112343400-112358000	Weak transcription	Pancreas	Pancrea
14	chr3:112344800-112350000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:112345000-112353800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr3:112345200-112359400	Weak transcription	Esophagus	oesophagus
17	chr3:112346000-112350400	Enhancers	Adipose Nuclei	Adipose
18	chr3:112346200-112349400	Enhancers	HUVEC	blood vessel
19	chr3:112346200-112352400	Weak transcription	Brain Anterior Caudate	brain
20	chr3:112346200-112352400	Weak transcription	Fetal Brain Female	brain
21	chr3:112346400-112354000	Weak transcription	Fetal Heart	heart
22	chr3:112346600-112348800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:112346600-112353800	Weak transcription	Aorta	Aorta
24	chr3:112346800-112349200	Enhancers	Fetal Stomach	stomach
25	chr3:112347000-112350000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:112347000-112351400	Genic enhancers	Osteobl	bone
27	chr3:112347200-112351200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:112347400-112349600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:112347400-112350600	Weak transcription	Fetal Intestine Large	intestine
30	chr3:112347400-112351600	Weak transcription	Ovary	ovary
31	chr3:112347600-112350000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:112347800-112348800	Weak transcription	NHLF	lung
33	chr3:112347800-112353200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr3:112348000-112351400	Enhancers	Colon Smooth Muscle	Colon
35	chr3:112348000-112353200	Enhancers	Rectal Smooth Muscle	rectum
36	chr3:112348200-112348800	Enhancers	H9 Cell Line	embryonic stem cell
37	chr3:112348200-112348800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:112348200-112348800	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr3:112348200-112348800	Enhancers	GM12878-XiMat	blood
40	chr3:112348200-112348800	Enhancers	Hela-S3	cervix
41	chr3:112348200-112349000	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr3:112348200-112349000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:112348200-112349000	Flanking Active TSS	A549	lung
44	chr3:112348200-112349000	Enhancers	HMEC	breast
45	chr3:112348200-112349000	Enhancers	NHEK	skin
46	chr3:112348200-112349200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:112348200-112349200	Genic enhancers	Placenta Amnion	Placenta Amnion
48	chr3:112348200-112349400	Enhancers	Stomach Smooth Muscle	stomach
49	chr3:112348200-112351400	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr3:112348200-112351600	Genic enhancers	HSMM	muscle

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