Variant report

Variant	rs589027
Chromosome Location	chr1:210505726-210505727
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210497683..210507034-chr1:210544536..210549319,22	MCF-7	breast:
2	chr1:210499363..210504206-chr1:210504461..210511314,11	MCF-7	breast:
3	chr1:210505702..210510006-chr1:210545251..210547944,5	K562	blood:
4	chr1:210498648..210506320-chr1:210545155..210548300,7	K562	blood:

Variant related genes	Relation type
ENSG00000054392	Chromatin interaction
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10489387	0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11119480	0.94[JPT][hapmap]
rs1883655	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2015743	0.82[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2103691	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2143590	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2294847	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2294848	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3765867	0.85[CHB][hapmap]
rs3765873	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs3765880	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3819987	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs4336853	0.85[CHB][hapmap]
rs590883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs642116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6540590	0.87[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs6540591	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs655213	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs684045	0.95[MKK][hapmap]
rs684767	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs761172	0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs764585	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs910028	0.83[ASN][1000 genomes]
rs9970232	0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs589027	LOC148696	cis	parietal	SCAN
rs589027	SELO	trans	cerebellum	SCAN
rs589027	SERTAD4	cis	cerebellum	SCAN
rs589027	ELK4	cis	parietal	SCAN
rs589027	YOD1	cis	cerebellum	SCAN
rs589027	TRAF3IP3	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210503000-210506000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:210503200-210506400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:210503200-210506600	Enhancers	Fetal Heart	heart
4	chr1:210503200-210507200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:210503200-210507400	Enhancers	Primary T cells fromperipheralblood	blood
6	chr1:210503200-210516800	Weak transcription	Lung	lung
7	chr1:210503600-210546800	Weak transcription	Fetal Intestine Small	intestine
8	chr1:210503800-210505800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:210504000-210506400	Weak transcription	Dnd41	blood
10	chr1:210504200-210505800	Weak transcription	HMEC	breast
11	chr1:210504200-210506000	Weak transcription	Left Ventricle	heart
12	chr1:210504200-210508200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:210504200-210512800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:210504400-210507200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:210504400-210514800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:210504400-210516400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:210504600-210507600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:210504800-210506600	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr1:210505200-210506600	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr1:210505200-210506800	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr1:210505200-210507400	Enhancers	Thymus	Thymus
22	chr1:210505400-210506000	Enhancers	Duodenum Mucosa	Duodenum
23	chr1:210505400-210506600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:210505400-210507000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:210505400-210507000	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr1:210505600-210505800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:210505600-210505800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:210505600-210506200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:210505600-210506200	Flanking Active TSS	GM12878-XiMat	blood
30	chr1:210505600-210506600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:210505600-210506600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:210505600-210506600	Enhancers	NHEK	skin
33	chr1:210505600-210506800	Enhancers	Primary B cells from peripheral blood	blood
34	chr1:210505600-210506800	Enhancers	Primary hematopoietic stem cells	blood
35	chr1:210505600-210506800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr1:210505600-210507200	Enhancers	Fetal Thymus	thymus

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