Variant report

Variant	rs4877751
Chromosome Location	chr9:85885299-85885300
allele	A/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	NFIC	chr9:85884699-85885302	ECC-1	luminal epithelium:	n/a	chr9:85884954-85884970
2	KAP1	chr9:85884875-85885340	HEK293	kidney:	n/a	n/a
3	GATA2	chr9:85884842-85885592	HUVEC	blood vessel:	n/a	chr9:85885240-85885256 chr9:85885240-85885256 chr9:85885243-85885253 chr9:85885245-85885255 chr9:85885234-85885251

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:85884317..85887181-chr9:85896355..85898967,2	MCF-7	breast:
2	chr9:85833317..85835949-chr9:85882469..85885385,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf103-5	chr9:85882090-85885748	NONHSAT132734

Variant related genes	Relation type
FRMD3	TF binding region
ENSG00000172159	Chromatin interaction
ENSG00000229109	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10117251	0.82[JPT][hapmap]
rs10118491	0.80[CHB][hapmap];0.81[CHD][hapmap];0.81[MEX][hapmap]
rs10780587	0.82[MEX][hapmap]
rs10867967	0.80[CEU][hapmap];0.83[ASN][1000 genomes]
rs10867973	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs10867975	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10867976	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10867977	0.88[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10867980	0.82[MEX][hapmap]
rs10867981	0.82[MEX][hapmap]
rs11140004	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs11140007	0.80[AMR][1000 genomes]
rs11795034	0.83[ASN][1000 genomes]
rs11795096	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs12339855	0.94[ASW][hapmap];0.83[YRI][hapmap]
rs1323776	0.80[AMR][1000 genomes]
rs1323784	0.84[ASN][1000 genomes]
rs1359168	0.82[MEX][hapmap]
rs1535750	0.82[MEX][hapmap]
rs1535752	0.88[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1535753	0.88[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1886125	0.81[MEX][hapmap]
rs1886126	0.87[CHD][hapmap]
rs2209186	0.81[CEU][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes]
rs2209187	0.96[CEU][hapmap];0.83[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2209188	0.96[CEU][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2378658	0.88[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2889954	0.83[JPT][hapmap]
rs3739658	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4418413	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7039712	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7039947	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72743036	0.83[ASN][1000 genomes]
rs7857494	0.89[ASN][1000 genomes]
rs942278	0.96[CEU][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs942279	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs942280	0.82[ASW][hapmap];0.96[CEU][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs942282	0.96[CEU][hapmap];0.83[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs942283	0.82[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]

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	nsv1046491	chr9:85861492-86063992	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv6586	chr9:85869828-85914812	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4877751	UBQLN1	cis	cerebellum	SCAN
rs4877751	C9orf153	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85854800-85890400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr9:85856200-85910600	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr9:85866200-85913000	Weak transcription	Aorta	Aorta
4	chr9:85881600-85889000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr9:85882000-85886600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr9:85882000-85895800	Weak transcription	Fetal Kidney	kidney
7	chr9:85882000-85895800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr9:85882200-85886600	Weak transcription	Adipose Nuclei	Adipose
9	chr9:85882200-85886600	Enhancers	Fetal Heart	heart
10	chr9:85882200-85887200	Enhancers	HUVEC	blood vessel
11	chr9:85882200-85889400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr9:85882200-85889400	Weak transcription	Fetal Stomach	stomach
13	chr9:85882200-85889800	Weak transcription	Pancreas	Pancrea
14	chr9:85882200-85895800	Weak transcription	Gastric	stomach
15	chr9:85882200-85895800	Weak transcription	Ovary	ovary
16	chr9:85882200-85896000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:85882400-85886400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr9:85883000-85886000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr9:85883000-85888600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr9:85883200-85895000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr9:85884200-85912400	Weak transcription	HepG2	liver
22	chr9:85884800-85885400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:85884800-85885400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:85884800-85885400	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr9:85884800-85885400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr9:85884800-85885400	Enhancers	Left Ventricle	heart
27	chr9:85884800-85885400	Enhancers	Right Ventricle	heart
28	chr9:85884800-85885600	Enhancers	Psoas Muscle	Psoas
29	chr9:85884800-85886000	Enhancers	Right Atrium	heart
30	chr9:85885000-85885400	Enhancers	Fetal Muscle Leg	muscle
31	chr9:85885000-85885400	Enhancers	Spleen	Spleen
32	chr9:85885000-85885600	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr9:85885000-85885800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr9:85885200-85885400	Enhancers	Brain Cingulate Gyrus	brain
35	chr9:85885200-85896600	Weak transcription	Brain Angular Gyrus	brain

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