Variant report

Variant	rs356685
Chromosome Location	chr9:97969659-97969660
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97968772..97971256-chr9:97972231..97974101,2	MCF-7	breast:
2	chr9:97960729..97962513-chr9:97968919..97971853,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1020962	1.00[JPT][hapmap]
rs1038092	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs10761371	1.00[JPT][hapmap]
rs10993471	1.00[JPT][hapmap]
rs1564235	1.00[JPT][hapmap]
rs1571896	1.00[JPT][hapmap]
rs1623009	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs173339	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1871220	1.00[JPT][hapmap]
rs1888944	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs2061798	1.00[JPT][hapmap]
rs2061801	1.00[JPT][hapmap]
rs242448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2655055	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2765817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs356660	0.86[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];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs356661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs356662	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs356663	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[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs356671	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[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs356686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3739748	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs3780560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs400727	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs420089	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4647379	1.00[MKK][hapmap];0.80[YRI][hapmap]
rs4647513	1.00[MKK][hapmap];1.00[YRI][hapmap]
rs4647551	1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[YRI][hapmap]
rs4743975	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs4743977	1.00[JPT][hapmap]
rs4743989	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4744437	0.91[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs4744440	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs475413	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs607105	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs648615	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs651009	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7033294	1.00[YRI][hapmap]
rs7049188	0.90[YRI][hapmap]
rs7866396	0.82[YRI][hapmap]
rs9299427	0.94[AMR][1000 genomes];0.89[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	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
2	nsv831657	chr9:97959274-98204769	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs356685	MIR23B	cis	lymphoblastoid	seeQTL
rs356685	TPM2	trans	lymphoblastoid	seeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97962000-97980600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:97963000-97993400	Weak transcription	Hela-S3	cervix
3	chr9:97964400-97971800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr9:97966800-97969800	Weak transcription	Lung	lung
5	chr9:97968400-97970200	Enhancers	Fetal Intestine Large	intestine
6	chr9:97968600-97976800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr9:97968800-97970200	Enhancers	A549	lung
8	chr9:97968800-97973400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr9:97969000-97969800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:97969000-97969800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr9:97969000-97969800	Enhancers	Fetal Stomach	stomach
12	chr9:97969000-97969800	Enhancers	NHDF-Ad	bronchial
13	chr9:97969000-97970000	Enhancers	Fetal Lung	lung
14	chr9:97969000-97970000	Enhancers	Small Intestine	intestine
15	chr9:97969000-97970000	Enhancers	HSMMtube	muscle
16	chr9:97969000-97973000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:97969000-97973400	Weak transcription	Fetal Kidney	kidney
18	chr9:97969200-97969800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr9:97969200-97969800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr9:97969400-97969800	Enhancers	Fetal Intestine Small	intestine
21	chr9:97969400-97970000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr9:97969400-97973200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr9:97969600-97969800	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr9:97969600-97970000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr9:97969600-97970000	Enhancers	HepG2	liver
26	chr9:97969600-97970200	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr9:97969600-97973400	Weak transcription	Ovary	ovary

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