Variant report

Variant	rs1537011
Chromosome Location	chr9:117820549-117820550
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr9:117819603-117820958	SK-N-SH	brain:	n/a	chr9:117820237-117820248
2	EP300	chr9:117819592-117821048	SK-N-SH	brain:	n/a	n/a
3	EP300	chr9:117820453-117820913	SK-N-SH_RA	brain:	n/a	n/a
4	TCF12	chr9:117819474-117821073	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr9:117819454-117821891	SK-N-SH	brain:	n/a	chr9:117819980-117819996 chr9:117819810-117819817
6	TEAD4	chr9:117819596-117820775	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr9:117819241-117822911	U87	brain:	n/a	n/a
8	TEAD4	chr9:117819656-117820997	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr9:117820394-117820698	SK-N-SH	brain:	n/a	n/a
10	RXRA	chr9:117819729-117820823	SK-N-SH	brain:	n/a	n/a
11	EP300	chr9:117820413-117820903	SK-N-SH_RA	brain:	n/a	n/a
12	NFIC	chr9:117819479-117821055	SK-N-SH	brain:	n/a	n/a
13	GATA3	chr9:117819547-117821092	SK-N-SH	brain:	n/a	chr9:117819980-117819996 chr9:117819810-117819817
14	PBX3	chr9:117820413-117820942	SK-N-SH	brain:	n/a	n/a
15	GATA3	chr9:117820509-117820830	T-47D	breast:	n/a	n/a
16	PBX3	chr9:117819647-117820929	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr9:117819591-117820872	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr9:117820318-117820976	U87	brain:	n/a	n/a
19	TCF12	chr9:117820448-117820948	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:117816355..117818608-chr9:117819773..117822159,2	K562	blood:

Variant related genes	Relation type
TNC	TF binding region
ENSG00000041982	Chromatin interaction

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

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

rs_ID	r²[population]
rs10117421	1.00[CHB][hapmap];0.96[TSI][hapmap]
rs1330361	1.00[CHB][hapmap];0.81[GIH][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17241078	1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17241442	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17241477	1.00[CHB][hapmap]
rs17819299	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17819466	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001357	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2150101	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28393206	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4549855	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56961588	0.84[AMR][1000 genomes]
rs57398199	0.84[AMR][1000 genomes]
rs62578423	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62578424	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62578425	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[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	nsv831696	chr9:117701582-117874150	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1537011	C9orf84	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117782400-117848200	Weak transcription	Brain Substantia Nigra	brain
2	chr9:117791600-117833200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:117800800-117825000	Weak transcription	Fetal Muscle Leg	muscle
4	chr9:117800800-117825200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr9:117802200-117848200	Weak transcription	Spleen	Spleen
6	chr9:117803400-117820600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:117803600-117825400	Weak transcription	Fetal Kidney	kidney
8	chr9:117809000-117825400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:117809200-117821000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:117810600-117825000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr9:117812800-117825800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr9:117812800-117830600	Weak transcription	Fetal Lung	lung
13	chr9:117813200-117825000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:117815200-117821000	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr9:117815200-117825200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:117815400-117859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr9:117816000-117825200	Weak transcription	Esophagus	oesophagus
18	chr9:117816600-117820600	Strong transcription	Colon Smooth Muscle	Colon
19	chr9:117816800-117825000	Strong transcription	Stomach Smooth Muscle	stomach
20	chr9:117817800-117850600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr9:117818800-117823200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr9:117819200-117821000	Enhancers	HMEC	breast
23	chr9:117819200-117822400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:117819200-117822600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:117819200-117827400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr9:117819400-117825800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr9:117819600-117821800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr9:117819600-117822800	Genic enhancers	Osteobl	bone
29	chr9:117819800-117820800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr9:117819800-117822000	Genic enhancers	NH-A	brain
31	chr9:117819800-117822200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr9:117819800-117822200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr9:117819800-117822600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:117819800-117822800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr9:117819800-117848000	Weak transcription	Fetal Intestine Small	intestine
36	chr9:117820000-117821000	Enhancers	Aorta	Aorta
37	chr9:117820200-117820600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr9:117820200-117821800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr9:117820200-117822400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr9:117820200-117822600	Enhancers	NHDF-Ad	bronchial
41	chr9:117820200-117822800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr9:117820200-117822800	Genic enhancers	NHLF	lung
43	chr9:117820200-117824600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr9:117820400-117820800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr9:117820400-117820800	Enhancers	Brain Cingulate Gyrus	brain
46	chr9:117820400-117820800	Enhancers	Fetal Stomach	stomach
47	chr9:117820400-117820800	Enhancers	HSMM	muscle
48	chr9:117820400-117822200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr9:117820400-117823400	Enhancers	NHEK	skin

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