Variant report

Variant	rs17541277
Chromosome Location	chr9:92686746-92686747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:92218872..92221885-chr9:92684149..92688442,4	MCF-7	breast:
2	chr9:92455398..92458346-chr9:92686302..92688067,2	MCF-7	breast:
3	chr9:92217841..92222641-chr9:92679830..92688712,19	MCF-7	breast:
4	chr9:92686545..92689268-chr9:92692416..92694064,2	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];0.89[ASN][1000 genomes]
rs10118987	1.00[MKK][hapmap]
rs10119039	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[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];0.89[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];0.89[ASN][1000 genomes]
rs16905902	0.92[ASN][1000 genomes]
rs16905907	0.93[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];0.89[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];0.89[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];0.89[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];1.00[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];0.89[ASN][1000 genomes]
rs4743958	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[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];0.89[ASN][1000 genomes]
rs4744475	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]
rs4744479	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4744480	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7029990	1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[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
rs17541277	SEMA4D	cis	cerebellum	SCAN
rs17541277	HHIP	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:92681600-92691600	Weak transcription	Right Atrium	heart
2	chr9:92681800-92689000	Weak transcription	Right Ventricle	heart
3	chr9:92682000-92689200	Weak transcription	Lung	lung
4	chr9:92683800-92689200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:92684400-92687400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr9:92684400-92687400	Enhancers	Placenta Amnion	Placenta Amnion
7	chr9:92685000-92687200	Enhancers	HepG2	liver
8	chr9:92685000-92690800	Enhancers	Liver	Liver
9	chr9:92685000-92691200	Weak transcription	Spleen	Spleen
10	chr9:92685200-92689200	Weak transcription	Gastric	stomach
11	chr9:92685400-92688600	Weak transcription	Fetal Brain Male	brain
12	chr9:92685800-92687000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr9:92686200-92686800	Enhancers	Fetal Intestine Small	intestine
14	chr9:92686200-92686800	Enhancers	Ovary	ovary
15	chr9:92686200-92687000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr9:92686200-92687000	Enhancers	Primary B cells from peripheral blood	blood
17	chr9:92686200-92687000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
18	chr9:92686200-92687000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr9:92686200-92687000	Enhancers	Fetal Intestine Large	intestine
20	chr9:92686200-92687000	Enhancers	Placenta	Placenta
21	chr9:92686200-92687400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr9:92686200-92689800	Enhancers	Pancreas	Pancrea
23	chr9:92686400-92686800	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr9:92686400-92686800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr9:92686400-92687000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr9:92686400-92687400	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr9:92686400-92689600	Weak transcription	Fetal Kidney	kidney
28	chr9:92686600-92686800	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr9:92686600-92688400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr9:92686600-92688800	Weak transcription	Fetal Heart	heart
31	chr9:92686600-92689200	Weak transcription	Fetal Lung	lung
32	chr9:92686600-92689200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr9:92686600-92691000	Weak transcription	Fetal Thymus	thymus
34	chr9:92686600-92691200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr9:92686600-92691400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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