Variant report

Variant	rs9508556
Chromosome Location	chr13:30380407-30380408
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:30373480..30375303-chr13:30379875..30382396,3	MCF-7	breast:
2	chr13:30378464..30380785-chr21:33103550..33105842,2	MCF-7	breast:
3	chr13:30351544..30354473-chr13:30379048..30380772,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156304	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs17073936	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs182178	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1886170	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2234417	1.00[CHD][hapmap]
rs2388244	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2388245	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278037	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs4769774	0.88[CHD][hapmap];0.91[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs7330373	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9314976	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899961	chr13:30226924-30407273	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9508556	MTUS2	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30363800-30385000	Weak transcription	Left Ventricle	heart
2	chr13:30365800-30383200	Weak transcription	Ovary	ovary
3	chr13:30366200-30381400	Weak transcription	Stomach Mucosa	stomach
4	chr13:30373400-30383200	Weak transcription	Small Intestine	intestine
5	chr13:30374200-30380800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr13:30374200-30383200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr13:30375400-30383200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr13:30376200-30380600	Weak transcription	Brain Angular Gyrus	brain
9	chr13:30376200-30381400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr13:30376200-30384200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr13:30376400-30383200	Weak transcription	Brain Anterior Caudate	brain
12	chr13:30376400-30383400	Weak transcription	Gastric	stomach
13	chr13:30376400-30386000	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr13:30376600-30380600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr13:30376600-30380600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr13:30376600-30381400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr13:30376600-30383600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr13:30376600-30383800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr13:30376600-30383800	Weak transcription	Right Atrium	heart
20	chr13:30376600-30384000	Weak transcription	Colon Smooth Muscle	Colon
21	chr13:30376600-30385200	Weak transcription	Lung	lung
22	chr13:30376600-30385600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr13:30376600-30420600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr13:30376800-30381400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr13:30376800-30383400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr13:30377000-30380600	Weak transcription	Liver	Liver
27	chr13:30377000-30381400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr13:30377200-30380600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr13:30377200-30383600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr13:30377400-30383200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr13:30377400-30390000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr13:30377600-30381600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr13:30377600-30384400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr13:30377800-30384600	Weak transcription	Osteobl	bone
35	chr13:30378000-30391800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr13:30378400-30383200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr13:30378800-30384800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr13:30379000-30381400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr13:30379200-30381600	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr13:30379200-30383200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr13:30379600-30380600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr13:30379600-30380800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr13:30380000-30381600	Enhancers	Pancreas	Pancrea
44	chr13:30380200-30380800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr13:30380200-30382400	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr13:30380200-30383600	Weak transcription	Psoas Muscle	Psoas
47	chr13:30380400-30380800	Enhancers	Brain Substantia Nigra	brain
48	chr13:30380400-30381000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr13:30380400-30381000	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr13:30380400-30381600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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