Variant report

Variant	rs13082485
Chromosome Location	chr3:178908580-178908581
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:178900635..178902504-chr3:178907867..178909492,2	MCF-7	breast:
2	chr3:178903831..178906930-chr3:178907124..178910138,3	K562	blood:
3	chr3:23957347..23958990-chr3:178908565..178910947,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174748	Chromatin interaction
ENSG00000197885	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1170673	0.81[CEU][hapmap]
rs13099856	1.00[ASN][1000 genomes]
rs1517586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542298	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2677763	1.00[ASN][1000 genomes]
rs2677764	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2677770	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2699887	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2699891	0.91[ASN][1000 genomes]
rs2699893	0.97[ASN][1000 genomes]
rs2699905	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2699906	1.00[ASN][1000 genomes]
rs4955801	0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6784495	0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs73187259	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9968179	0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][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	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13082485	DTNA	trans	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178887200-178912000	Weak transcription	Thymus	Thymus
2	chr3:178896800-178912200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr3:178896800-178912400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr3:178897800-178919400	Weak transcription	Fetal Intestine Small	intestine
5	chr3:178899200-178951800	Weak transcription	K562	blood
6	chr3:178900000-178929800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:178900400-178912200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr3:178900400-178912400	Weak transcription	NH-A	brain
9	chr3:178900600-178912000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:178900600-178912000	Weak transcription	Left Ventricle	heart
11	chr3:178900600-178912200	Weak transcription	Pancreas	Pancrea
12	chr3:178900800-178912400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr3:178900800-178913400	Weak transcription	Osteobl	bone
14	chr3:178901000-178913200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr3:178901200-178912600	Weak transcription	Liver	Liver
16	chr3:178902800-178912000	Weak transcription	Fetal Thymus	thymus
17	chr3:178904000-178918600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:178904400-178912400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr3:178904400-178912800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:178904400-178912800	Weak transcription	Brain Substantia Nigra	brain
21	chr3:178904600-178913000	Weak transcription	Primary B cells from cord blood	blood
22	chr3:178904800-178916400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:178905000-178912200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:178905800-178909000	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr3:178906000-178909000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr3:178906000-178909200	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr3:178906200-178912200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:178906400-178912600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:178906400-178962400	Weak transcription	HepG2	liver
30	chr3:178906600-178909200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr3:178906800-178910000	Enhancers	Fetal Stomach	stomach
32	chr3:178907000-178909000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:178907200-178908600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:178907200-178908600	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr3:178907200-178908800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:178907200-178908800	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr3:178907200-178908800	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr3:178907200-178909000	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr3:178907200-178909200	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr3:178907200-178909200	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr3:178907200-178909200	Enhancers	Fetal Kidney	kidney
42	chr3:178907200-178909200	Enhancers	Rectal Smooth Muscle	rectum
43	chr3:178907200-178909400	Enhancers	Fetal Lung	lung
44	chr3:178907400-178908800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:178907400-178908800	Enhancers	Brain Hippocampus Middle	brain
46	chr3:178907400-178909000	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr3:178907400-178909000	Enhancers	Ovary	ovary
48	chr3:178907400-178909200	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr3:178907600-178908600	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr3:178907600-178908600	Enhancers	iPS-20b Cell Line	embryonic stem cell

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