Variant report

Variant	rs11749561
Chromosome Location	chr5:142791677-142791678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:142783356..142786232-chr5:142789079..142791701,2	MCF-7	breast:
2	chr5:142789222..142791860-chr5:142794676..142796552,2	K562	blood:
3	chr5:142788694..142792044-chr5:142796699..142799273,3	K562	blood:
4	chr5:142783227..142787898-chr5:142788004..142797496,15	K562	blood:
5	chr5:142788011..142789886-chr5:142791170..142792935,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113580	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10052957	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1438732	1.00[JPT][hapmap]
rs1837262	1.00[JPT][hapmap]
rs1866388	1.00[JPT][hapmap]
rs190488	1.00[JPT][hapmap]
rs2043840	1.00[JPT][hapmap]
rs258750	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs258753	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs258813	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2918415	1.00[JPT][hapmap]
rs2918416	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2918417	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2918418	1.00[JPT][hapmap]
rs2918419	1.00[JPT][hapmap]
rs2963149	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2963151	1.00[JPT][hapmap]
rs2963153	0.85[ASN][1000 genomes]
rs2963154	1.00[JPT][hapmap]
rs33389	1.00[JPT][hapmap]
rs6188	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6194	1.00[JPT][hapmap]
rs6196	1.00[JPT][hapmap]
rs6861962	1.00[JPT][hapmap]
rs712189	0.86[JPT][hapmap]
rs72801096	0.90[ASN][1000 genomes]
rs852975	0.83[ASN][1000 genomes]
rs852977	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs852978	1.00[JPT][hapmap]
rs852982	1.00[JPT][hapmap]
rs853157	0.85[JPT][hapmap]
rs853184	1.00[JPT][hapmap]
rs860457	1.00[JPT][hapmap]
rs864082	1.00[JPT][hapmap]
rs9324918	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023976	chr5:142692062-142813664	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv882994	chr5:142770135-142791677	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11749561	HDAC3	cis	parietal	SCAN
rs11749561	HDAC3	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:142785000-142798200	Weak transcription	Spleen	Spleen
2	chr5:142785400-142795800	Weak transcription	Small Intestine	intestine
3	chr5:142785600-142793200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr5:142785600-142793400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr5:142785600-142795800	Weak transcription	Pancreas	Pancrea
6	chr5:142786200-142792200	Weak transcription	NHDF-Ad	bronchial
7	chr5:142786200-142792800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr5:142786200-142796000	Weak transcription	HepG2	liver
9	chr5:142788000-142792800	Weak transcription	GM12878-XiMat	blood
10	chr5:142789000-142796000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr5:142789000-142796200	Enhancers	Dnd41	blood
12	chr5:142790400-142811800	Weak transcription	Primary T cells from cord blood	blood
13	chr5:142790800-142792800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr5:142791200-142792200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:142791400-142791800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr5:142791400-142791800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr5:142791400-142792000	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr5:142791400-142792000	Enhancers	H1 Cell Line	embryonic stem cell
19	chr5:142791400-142792000	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr5:142791400-142792200	Enhancers	Liver	Liver
21	chr5:142791400-142792800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:142791400-142794200	Enhancers	Hela-S3	cervix
23	chr5:142791600-142792000	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr5:142791600-142792000	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr5:142791600-142792000	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr5:142791600-142792000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:142791600-142792400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr5:142791600-142792800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:142791600-142792800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:142791600-142793000	Enhancers	A549	lung
31	chr5:142791600-142798000	Weak transcription	Gastric	stomach

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