Variant report

Variant	rs236489
Chromosome Location	chr6:36685577-36685578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36645600..36648162-chr6:36684674..36687564,2	K562	blood:
2	chr6:36684189..36687540-chr6:36688167..36692245,5	MCF-7	breast:
3	chr6:36587328..36589112-chr6:36683598..36686485,2	MCF-7	breast:
4	chr6:36644040..36648031-chr6:36680924..36685784,5	MCF-7	breast:
5	chr6:36682230..36683943-chr6:36684153..36685768,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255587	Chromatin interaction
ENSG00000124762	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1864750	0.87[CHD][hapmap]
rs236452	0.87[CHD][hapmap]
rs236478	0.89[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs236480	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs236481	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs236482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236483	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[ASN][1000 genomes]
rs236487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236490	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[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	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs236489	SNRPC	cis	cerebellum	SCAN
rs236489	SRSF3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36661400-36696400	Weak transcription	Right Atrium	heart
2	chr6:36671800-36694000	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr6:36672200-36693600	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr6:36677000-36694000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr6:36681400-36688800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:36682000-36686400	Strong transcription	Spleen	Spleen
7	chr6:36682000-36686800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:36682200-36686200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:36682400-36687000	Weak transcription	GM12878-XiMat	blood
10	chr6:36683200-36686400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:36683600-36686400	Enhancers	Esophagus	oesophagus
12	chr6:36683800-36689400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:36683800-36695200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr6:36684200-36685600	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr6:36684400-36686000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:36684600-36685600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:36684600-36685800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:36684600-36686000	Enhancers	Fetal Muscle Leg	muscle
19	chr6:36684600-36686200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr6:36685000-36686200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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