Variant report

Variant	rs912580
Chromosome Location	chr6:147202606-147202607
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:147200323..147203212-chr6:147234929..147236464,2	MCF-7	breast:
2	chr6:147201123..147203183-chr6:147520675..147522289,2	K562	blood:
3	chr6:147200700..147210109-chr6:147522792..147529002,17	K562	blood:

Variant related genes	Relation type
ENSG00000233452	Chromatin interaction
ENSG00000164506	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1022877	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs1122570	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs1324684	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1467623	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1966195	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1998641	0.83[JPT][hapmap]
rs4605907	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4895704	0.88[JPT][hapmap]
rs4896895	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724774	0.83[JPT][hapmap]
rs7752595	0.85[YRI][hapmap]
rs877660	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912577	0.88[JPT][hapmap]
rs912581	0.82[ASN][1000 genomes]
rs9373515	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9390434	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9390436	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[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	nsv830838	chr6:147090745-147274669	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs912580	KATNA1	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:147198000-147203000	Weak transcription	Small Intestine	intestine
2	chr6:147198200-147203600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:147198200-147205600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:147198800-147202800	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr6:147200000-147205600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:147200200-147204800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:147200200-147205000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:147200200-147205400	Weak transcription	Liver	Liver
9	chr6:147200200-147208600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr6:147200400-147204800	Weak transcription	Fetal Intestine Small	intestine
11	chr6:147200400-147205000	Weak transcription	Fetal Intestine Large	intestine
12	chr6:147200600-147202800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:147200800-147203200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:147200800-147205000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:147201200-147208000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr6:147201400-147205000	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr6:147202000-147203200	Flanking Active TSS	K562	blood
18	chr6:147202200-147203200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:147202200-147203200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr6:147202200-147212400	Weak transcription	Primary hematopoietic stem cells	blood

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