Variant report

Variant	rs11700338
Chromosome Location	chr20:25595868-25595869
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25594825..25598206-chr20:25602674..25604770,4	MCF-7	breast:
2	chr20:25591410..25597359-chr20:25600309..25606040,12	K562	blood:
3	chr20:25593129..25595979-chr20:25604532..25607057,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213742	Chromatin interaction
ENSG00000170191	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11087526	0.87[ASN][1000 genomes]
rs11698953	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11698992	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11699872	0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs11700297	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12480853	0.83[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs12481037	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12625991	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1343355	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1546890	0.88[ASN][1000 genomes]
rs16987966	0.87[ASN][1000 genomes]
rs1888037	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2050097	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2281212	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.83[MKK][hapmap]
rs3736720	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3764694	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap]
rs4813576	0.84[ASN][1000 genomes]
rs4815438	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs55792313	0.82[ASN][1000 genomes]
rs57803591	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6037190	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6050690	0.83[CHB][hapmap]
rs6115202	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs6115227	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7260957	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs73597820	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73597824	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS 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	23 gene(s)	inside rSNPs	diseases
3	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv2762069	chr20:25506582-25619528	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11700338	KIAA0980	cis	multi-tissue	Pritchard
rs11700338	NINL	cis	cerebellum	SCAN
rs11700338	NINL	cis	parietal	SCAN
rs11700338	PYGB	cis	cerebellum	SCAN
rs11700338	ABHD12	cis	Temporal Cortex	GTEx
rs11700338	C20orf22	cis	multi-tissue	Pritchard
rs11700338	GINS1	cis	parietal	SCAN
rs11700338	HDHD4	cis	multi-tissue	Pritchard
rs11700338	ABHD12	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25580200-25603000	Weak transcription	Fetal Brain Male	brain
2	chr20:25581800-25603800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:25582000-25602800	Weak transcription	Osteobl	bone
4	chr20:25586000-25602600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr20:25586200-25602800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr20:25587000-25603000	Weak transcription	HSMMtube	muscle
7	chr20:25587400-25600400	Weak transcription	K562	blood
8	chr20:25587600-25601400	Weak transcription	Pancreas	Pancrea
9	chr20:25588400-25597800	Strong transcription	Dnd41	blood
10	chr20:25588400-25599200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr20:25588600-25596200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr20:25588600-25599400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr20:25588600-25599400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr20:25588600-25602800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr20:25589200-25601000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr20:25589200-25602600	Weak transcription	Right Ventricle	heart
17	chr20:25590800-25602600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr20:25590800-25603200	Weak transcription	Fetal Intestine Large	intestine
19	chr20:25591000-25603600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr20:25591400-25602800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr20:25591600-25600200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr20:25591600-25602800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr20:25591600-25603000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr20:25591600-25603200	Weak transcription	Fetal Lung	lung
25	chr20:25592200-25597200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr20:25592200-25602600	Weak transcription	Colon Smooth Muscle	Colon
27	chr20:25592200-25602600	Weak transcription	NHLF	lung
28	chr20:25592200-25602800	Weak transcription	Small Intestine	intestine
29	chr20:25592200-25602800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr20:25592200-25603200	Weak transcription	Brain Germinal Matrix	brain
31	chr20:25592600-25597600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr20:25592600-25602800	Weak transcription	Esophagus	oesophagus
33	chr20:25592600-25603200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr20:25592800-25603200	Weak transcription	Fetal Kidney	kidney
35	chr20:25592800-25603200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr20:25593000-25596400	Weak transcription	NHEK	skin
37	chr20:25593000-25597000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr20:25593000-25597000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr20:25593000-25597000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr20:25593000-25597400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr20:25593000-25597600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr20:25593000-25602800	Weak transcription	NH-A	brain
43	chr20:25593200-25596400	Weak transcription	NHDF-Ad	bronchial
44	chr20:25593200-25597000	Strong transcription	Adipose Nuclei	Adipose
45	chr20:25593200-25600400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr20:25593400-25597200	Strong transcription	HUVEC	blood vessel
47	chr20:25593600-25596000	Strong transcription	Left Ventricle	heart
48	chr20:25593600-25597000	Strong transcription	HepG2	liver
49	chr20:25593600-25602800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr20:25593800-25596000	Strong transcription	Fetal Muscle Leg	muscle

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