Variant report

Variant	rs10113929
Chromosome Location	chr9:72027641-72027642
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71939359..71941808-chr9:72025736..72028094,2	MCF-7	breast:
2	chr9:72027288..72028201-chr9:72161004..72161637,2	MCF-7	breast:
3	chr9:72005489..72008452-chr9:72026108..72027745,2	K562	blood:
4	chr9:72027335..72027966-chr9:72164135..72164934,2	MCF-7	breast:
5	chr9:71907137..71907714-chr9:72027328..72028069,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135063	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10046829	1.00[ASN][1000 genomes]
rs10113949	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10114017	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119925	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10120442	1.00[ASN][1000 genomes]
rs10124296	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11138512	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11138569	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12350476	1.00[ASN][1000 genomes]
rs1331971	1.00[ASN][1000 genomes]
rs17064047	1.00[MEX][hapmap]
rs28386177	1.00[ASN][1000 genomes]
rs28483200	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28505427	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35386391	1.00[EUR][1000 genomes]
rs41306153	1.00[EUR][1000 genomes]
rs4387043	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4475564	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535801	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73459173	1.00[ASN][1000 genomes]
rs73459178	1.00[ASN][1000 genomes]
rs73459180	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73647208	1.00[ASN][1000 genomes]
rs73647211	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7857199	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7870449	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7870559	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv893428	chr9:71926658-72027641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv893429	chr9:71961923-72047337	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv893430	chr9:71968730-72036369	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1035633	chr9:71995963-72176984	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv893431	chr9:72003036-72048098	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv8522	chr9:72009272-72034735	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv2757340	chr9:72018246-72048098	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv2759694	chr9:72018246-72048098	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10113929	FHL1	trans	lymphoblastoid	seeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72010000-72027800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:72013200-72027800	Weak transcription	Brain Substantia Nigra	brain
3	chr9:72026400-72027800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:72026600-72027800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:72026800-72028000	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr9:72026800-72028400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:72027000-72027800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr9:72027000-72028000	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr9:72027000-72028000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:72027000-72028000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr9:72027000-72028200	Enhancers	H1 Cell Line	embryonic stem cell
12	chr9:72027000-72028400	Enhancers	Esophagus	oesophagus
13	chr9:72027000-72040000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:72027200-72028000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr9:72027200-72028000	Enhancers	Fetal Heart	heart
16	chr9:72027200-72028000	Enhancers	Right Ventricle	heart
17	chr9:72027400-72027800	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr9:72027400-72027800	Active TSS	Osteobl	bone
19	chr9:72027400-72028000	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr9:72027400-72028000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr9:72027400-72028000	Enhancers	Brain Hippocampus Middle	brain
22	chr9:72027400-72028200	Enhancers	Fetal Lung	lung
23	chr9:72027600-72027800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:72027600-72027800	Bivalent Enhancer	Fetal Stomach	stomach
25	chr9:72027600-72027800	Weak transcription	Right Atrium	heart
26	chr9:72027600-72027800	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr9:72027600-72027800	Active TSS	Stomach Smooth Muscle	stomach
28	chr9:72027600-72027800	Enhancers	NHLF	lung
29	chr9:72027600-72028000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:72027600-72028000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr9:72027600-72028000	Active TSS	Brain Germinal Matrix	brain
32	chr9:72027600-72028000	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr9:72027600-72028000	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr9:72027600-72028000	Active TSS	Fetal Brain Female	brain
35	chr9:72027600-72028000	Enhancers	Fetal Muscle Leg	muscle
36	chr9:72027600-72028000	Enhancers	Rectal Smooth Muscle	rectum
37	chr9:72027600-72028000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr9:72027600-72028200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr9:72027600-72028200	Active TSS	Adipose Nuclei	Adipose
40	chr9:72027600-72028200	Enhancers	Ovary	ovary

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