Variant report

Variant	rs2357587
Chromosome Location	chr1:210592577-210592578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210590026..210592841-chr1:211432035..211434761,3	MCF-7	breast:
2	chr1:210583255..210586128-chr1:210592478..210594714,2	MCF-7	breast:
3	chr1:210542938..210544518-chr1:210591171..210592878,2	MCF-7	breast:
4	chr1:210545312..210548912-chr1:210591590..210593685,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200972	Chromatin interaction
ENSG00000117625	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10863826	0.81[ASN][1000 genomes]
rs10863829	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11119486	0.97[ASN][1000 genomes]
rs11119489	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11119491	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11119492	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11119497	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12043880	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12117930	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12136541	0.89[CEU][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12738703	0.95[CHB][hapmap];0.82[JPT][hapmap];0.99[ASN][1000 genomes]
rs2092448	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2357588	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3753226	0.94[ASW][hapmap];0.89[CEU][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4400614	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4601592	0.83[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.80[LWK][hapmap];0.99[ASN][1000 genomes]
rs4845019	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845021	0.88[ASW][hapmap];0.89[CEU][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4845023	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4845024	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4845025	0.86[MKK][hapmap];0.83[AFR][1000 genomes]
rs57153723	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6682398	0.97[ASN][1000 genomes]
rs7518269	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7538194	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8179439	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs926579	0.94[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.99[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	esv2756883	chr1:210579523-210620779	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	esv2758995	chr1:210579523-210620779	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2357587	SNORA16B	cis	parietal	SCAN
rs2357587	SLC45A3	cis	cerebellum	SCAN
rs2357587	HHAT	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210567400-210617200	Weak transcription	Left Ventricle	heart
2	chr1:210570200-210594000	Weak transcription	Fetal Lung	lung
3	chr1:210571400-210641000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:210573800-210594400	Weak transcription	Spleen	Spleen
5	chr1:210574400-210594400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:210574400-210595200	Weak transcription	Right Ventricle	heart
7	chr1:210585200-210593600	Weak transcription	Fetal Stomach	stomach
8	chr1:210586400-210610800	Weak transcription	Aorta	Aorta
9	chr1:210589400-210592800	Enhancers	HSMM	muscle
10	chr1:210589600-210592600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:210590200-210592800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:210591000-210592800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:210591800-210592800	Enhancers	Stomach Mucosa	stomach
14	chr1:210592000-210593000	Enhancers	HSMMtube	muscle
15	chr1:210592000-210609400	Weak transcription	Ovary	ovary
16	chr1:210592200-210593000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:210592200-210593000	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr1:210592200-210593000	Enhancers	A549	lung
19	chr1:210592400-210592600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:210592400-210592600	Enhancers	Fetal Intestine Small	intestine
21	chr1:210592400-210592800	Enhancers	Fetal Intestine Large	intestine
22	chr1:210592400-210593000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:210592400-210593000	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr1:210592400-210593400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:210592400-210593400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:210592400-210593600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:210592400-210593600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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