Variant report

Variant	rs6540593
Chromosome Location	chr1:210572589-210572590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:210544698..210555948-chr1:210566953..210584306,65	MCF-7	breast:
2	chr1:210566055..210568677-chr1:210572512..210575312,3	MCF-7	breast:
3	chr1:210572425..210575594-chr1:210579116..210581300,3	K562	blood:
4	chr1:210572567..210575023-chr1:211309974..211312335,2	MCF-7	breast:
5	chr1:210544801..210552702-chr1:210569747..210575327,18	MCF-7	breast:
6	chr1:210565121..210568359-chr1:210572172..210574144,3	K562	blood:
7	chr1:210551526..210553574-chr1:210572140..210575060,2	K562	blood:
8	chr1:210546689..210549252-chr1:210570902..210574338,5	K562	blood:
9	chr1:210533311..210536589-chr1:210572457..210575177,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000200972	Chromatin interaction
ENSG00000054392	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11119482	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2066721	0.84[LWK][hapmap];0.87[MKK][hapmap]
rs2073039	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2076516	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2143441	0.91[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3765863	0.91[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4844525	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4844526	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4844527	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap]
rs4845011	0.89[EUR][1000 genomes]
rs6540592	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6663590	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6685791	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6693035	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6693338	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6540593	ELK4	cis	cerebellum	SCAN
rs6540593	HHAT	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210529600-210586000	Weak transcription	Pancreas	Pancrea
2	chr1:210551400-210586000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:210559000-210584400	Weak transcription	Fetal Stomach	stomach
4	chr1:210566800-210586200	Weak transcription	Lung	lung
5	chr1:210567400-210617200	Weak transcription	Left Ventricle	heart
6	chr1:210568200-210572600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:210568200-210573800	Weak transcription	Aorta	Aorta
8	chr1:210568800-210573800	Weak transcription	Osteobl	bone
9	chr1:210569200-210573600	Weak transcription	HepG2	liver
10	chr1:210569400-210573600	Weak transcription	Right Ventricle	heart
11	chr1:210570200-210573400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:210570200-210594000	Weak transcription	Fetal Lung	lung
13	chr1:210570400-210574400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:210571200-210573200	Weak transcription	GM12878-XiMat	blood
15	chr1:210571200-210573800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:210571200-210573800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:210571200-210573800	Weak transcription	Right Atrium	heart
18	chr1:210571200-210586200	Weak transcription	Colonic Mucosa	Colon
19	chr1:210571200-210592400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:210571400-210572600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:210571400-210573200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:210571400-210573600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:210571400-210573800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:210571400-210574200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:210571400-210591400	Weak transcription	Ovary	ovary
26	chr1:210571400-210641000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:210571800-210573400	Weak transcription	HSMM	muscle
28	chr1:210571800-210573800	Weak transcription	HSMMtube	muscle

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