Variant report

Variant	rs2979269
Chromosome Location	chr8:8901140-8901141
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1045528	0.89[YRI][hapmap]
rs13249731	0.95[YRI][hapmap]
rs13263480	1.00[YRI][hapmap]
rs13273769	0.84[YRI][hapmap]
rs1430931	0.88[YRI][hapmap]
rs4841087	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4841088	0.86[LWK][hapmap];1.00[YRI][hapmap]
rs6993811	0.84[YRI][hapmap]
rs7816450	0.84[YRI][hapmap]
rs9650628	0.95[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv831229	chr8:8751523-8926235	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2979269	THEX1	Cis_1M	lymphoblastoid	RTeQTL
rs2979269	CLDN23	cis	multi-tissue	Pritchard
rs2979269	SGK223	cis	cerebellum	SCAN
rs2979269	CTSB	cis	parietal	SCAN
rs2979269	DEFB136	cis	parietal	SCAN
rs2979269	CTSB	cis	cerebellum	SCAN
rs2979269	MFHAS1	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8861400-8907000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:8861800-8915600	Weak transcription	Pancreas	Pancrea
3	chr8:8875400-8901200	Weak transcription	Thymus	Thymus
4	chr8:8877000-8903400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr8:8883600-8902400	Weak transcription	Adipose Nuclei	Adipose
6	chr8:8883800-8906000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr8:8884000-8906200	Weak transcription	Psoas Muscle	Psoas
8	chr8:8888400-8910800	Weak transcription	Hela-S3	cervix
9	chr8:8891000-8914800	Weak transcription	Fetal Stomach	stomach
10	chr8:8891400-8915200	Weak transcription	K562	blood
11	chr8:8892000-8901800	Weak transcription	Primary B cells from cord blood	blood
12	chr8:8893800-8913800	Weak transcription	Primary T cells from cord blood	blood
13	chr8:8897800-8902400	Enhancers	Placenta Amnion	Placenta Amnion
14	chr8:8898000-8902000	Weak transcription	GM12878-XiMat	blood
15	chr8:8898600-8905200	Weak transcription	Fetal Muscle Leg	muscle
16	chr8:8898600-8908800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr8:8898800-8903800	Weak transcription	Fetal Heart	heart
18	chr8:8898800-8907200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr8:8899000-8919200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr8:8899800-8902600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr8:8899800-8907200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr8:8900000-8907000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr8:8900000-8907200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr8:8900200-8902200	Weak transcription	Placenta	Placenta
25	chr8:8900200-8903200	Enhancers	NHEK	skin
26	chr8:8900200-8903800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr8:8900400-8901200	Enhancers	HMEC	breast
28	chr8:8900400-8903600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr8:8900400-8905600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr8:8900600-8901800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr8:8900600-8907200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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