Variant report

Variant	rs7035163
Chromosome Location	chr9:71386041-71386042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10511963	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs10869360	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs10869442	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs11143607	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11143636	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12350270	0.82[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.86[YRI][hapmap];0.92[ASN][1000 genomes]
rs1336492	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1412986	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[ASN][1000 genomes]
rs2027204	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2152647	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs4504703	0.82[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4745237	0.86[EUR][1000 genomes]
rs4745295	0.81[CEU][hapmap]
rs7033278	0.82[CEU][hapmap]
rs7853795	0.92[ASN][1000 genomes]
rs7864097	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs8114	0.91[GIH][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs952589	0.83[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][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	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7035163	SAMSN1	trans	lymphoblastoid	seeQTL
rs7035163	FAM122A	cis	Liver	GTEx
rs7035163	TJP2	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71374000-71388800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr9:71378000-71388400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr9:71378400-71394200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:71378800-71393800	Weak transcription	Primary B cells from cord blood	blood
5	chr9:71378800-71393800	Weak transcription	Primary B cells from peripheral blood	blood
6	chr9:71379000-71389000	Weak transcription	K562	blood
7	chr9:71383000-71388800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:71383600-71393800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr9:71383800-71393600	Weak transcription	Left Ventricle	heart
10	chr9:71384000-71386400	Weak transcription	Fetal Heart	heart
11	chr9:71384000-71394200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr9:71384400-71386200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:71384600-71386400	Enhancers	Stomach Mucosa	stomach
14	chr9:71384600-71387200	Enhancers	Fetal Intestine Large	intestine
15	chr9:71385000-71386200	Enhancers	Placenta	Placenta
16	chr9:71385600-71393800	Weak transcription	Small Intestine	intestine
17	chr9:71385800-71393400	Weak transcription	Fetal Intestine Small	intestine
18	chr9:71385800-71393800	Weak transcription	Right Ventricle	heart
19	chr9:71386000-71386200	Enhancers	Primary hematopoietic stem cells	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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