Variant report

Variant	rs4744475
Chromosome Location	chr9:92686142-92686143
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:92206823..92209475-chr9:92684160..92686501,2	MCF-7	breast:
2	chr9:92218872..92221885-chr9:92684149..92688442,4	MCF-7	breast:
3	chr9:92217841..92222641-chr9:92679830..92688712,19	MCF-7	breast:
4	chr14:96564791..96565302-chr9:92685623..92686143,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130222	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10115379	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10118987	1.00[MKK][hapmap]
rs10119039	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10821059	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10992652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16905902	0.96[ASN][1000 genomes]
rs16905907	0.96[ASN][1000 genomes]
rs16906012	1.00[ASW][hapmap]
rs17443508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17540718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17540745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17541277	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17541305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4743950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4743958	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4743964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4744479	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4744480	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7029990	1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][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	esv15329	chr9:92678855-92698160	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv3399737	chr9:92682932-92687130	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4744475	SEMA4D	cis	cerebellum	SCAN
rs4744475	HHIP	trans	lymphoblastoid	seeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:92681600-92691600	Weak transcription	Right Atrium	heart
2	chr9:92681800-92686200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:92681800-92686200	Weak transcription	Fetal Intestine Large	intestine
4	chr9:92681800-92686200	Weak transcription	Fetal Intestine Small	intestine
5	chr9:92681800-92686200	Weak transcription	Placenta	Placenta
6	chr9:92681800-92686200	Weak transcription	Left Ventricle	heart
7	chr9:92681800-92689000	Weak transcription	Right Ventricle	heart
8	chr9:92682000-92689200	Weak transcription	Lung	lung
9	chr9:92683800-92689200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:92684400-92687400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:92684400-92687400	Enhancers	Placenta Amnion	Placenta Amnion
12	chr9:92685000-92687200	Enhancers	HepG2	liver
13	chr9:92685000-92690800	Enhancers	Liver	Liver
14	chr9:92685000-92691200	Weak transcription	Spleen	Spleen
15	chr9:92685200-92686200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:92685200-92686200	Weak transcription	Fetal Heart	heart
17	chr9:92685200-92686200	Weak transcription	Fetal Kidney	kidney
18	chr9:92685200-92686200	Weak transcription	Fetal Lung	lung
19	chr9:92685200-92686200	Weak transcription	Pancreas	Pancrea
20	chr9:92685200-92689200	Weak transcription	Gastric	stomach
21	chr9:92685400-92688600	Weak transcription	Fetal Brain Male	brain
22	chr9:92685600-92686200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr9:92685600-92686200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
24	chr9:92685800-92687000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr9:92686000-92686400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:92686000-92686600	Enhancers	HUES6 Cell Line	embryonic stem cell

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