Variant report

Variant	rs4670989
Chromosome Location	chr2:40147610-40147611
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12712663	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12712664	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1547968	0.96[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1547969	0.88[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17024581	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17481747	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17481775	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17541280	0.85[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2110676	0.88[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2215972	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2373704	0.84[CEU][hapmap];0.93[CHB][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4670988	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7567740	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.99[ASN][1000 genomes]
rs7568751	0.88[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7575765	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003593	chr2:40009597-40165666	Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535651	chr2:40009597-40165666	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv873891	chr2:40046658-40173905	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv916300	chr2:40079899-40339019	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1003896	chr2:40094081-40231585	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1010609	chr2:40107234-40231674	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv535652	chr2:40107234-40231674	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv998885	chr2:40123904-40182851	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv873893	chr2:40137942-40222206	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv873894	chr2:40139250-40198380	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv873895	chr2:40139250-40207338	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv873896	chr2:40139250-40208665	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv873897	chr2:40139250-40225253	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv963910	chr2:40139364-40155674	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv869668	chr2:40141079-40249854	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv1003920	chr2:40141776-40245464	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv1000423	chr2:40143646-40245464	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4670989	SRSF7	cis	parietal	SCAN
rs4670989	SLC8A1	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40138400-40150400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr2:40138400-40150800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr2:40141600-40164800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:40142000-40147800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:40142200-40148000	Weak transcription	Fetal Stomach	stomach
6	chr2:40145200-40147800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:40145400-40148200	Enhancers	HSMM	muscle
8	chr2:40146600-40149400	Enhancers	Thymus	Thymus
9	chr2:40146800-40148000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:40146800-40148200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:40146800-40149600	Flanking Active TSS	Dnd41	blood
12	chr2:40147000-40148000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:40147000-40148200	Enhancers	Primary T cells from cord blood	blood
14	chr2:40147000-40167400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:40147200-40147800	Enhancers	Fetal Muscle Trunk	muscle
16	chr2:40147200-40147800	Enhancers	Placenta Amnion	Placenta Amnion
17	chr2:40147400-40147800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:40147400-40148000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:40147400-40148200	Enhancers	H1 Cell Line	embryonic stem cell
20	chr2:40147600-40147800	Flanking Active TSS	Fetal Thymus	thymus
21	chr2:40147600-40148000	Enhancers	Primary B cells from cord blood	blood
22	chr2:40147600-40148000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:40147600-40148000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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