Variant report

Variant	rs10947441
Chromosome Location	chr6:33789581-33789582
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33756537..33758549-chr6:33788419..33790065,2	K562	blood:
2	chr6:33764770..33766513-chr6:33787828..33789808,2	K562	blood:
3	chr6:33788574..33790183-chr6:33793587..33795973,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161904	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10947432	1.00[LWK][hapmap];0.95[MKK][hapmap]
rs10947442	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947443	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10947445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755817	1.00[JPT][hapmap]
rs12189725	1.00[LWK][hapmap];0.95[MKK][hapmap]
rs12192087	0.80[AMR][1000 genomes]
rs12193658	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12198383	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12203688	1.00[LWK][hapmap];0.95[MKK][hapmap]
rs12211490	1.00[LWK][hapmap];0.95[MKK][hapmap]
rs13203745	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13204162	1.00[LWK][hapmap];0.95[MKK][hapmap]
rs13214874	1.00[LWK][hapmap];0.95[MKK][hapmap]
rs2274459	1.00[LWK][hapmap];0.95[MKK][hapmap]
rs2281831	0.86[MKK][hapmap]
rs2281918	0.95[MKK][hapmap]
rs2296340	1.00[JPT][hapmap]
rs34139560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34384116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34929964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36108476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818532	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap]
rs66617522	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72896150	0.88[ASN][1000 genomes]
rs72896152	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs877187	1.00[LWK][hapmap];0.90[MKK][hapmap]
rs9469554	0.95[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885773	chr6:33778964-33813043	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv885774	chr6:33778964-33840121	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv885775	chr6:33788055-33828178	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10947441	LEMD2	cis	parietal	SCAN
rs10947441	LEMD2	cis	cerebellum	SCAN
rs10947441	C6orf227	cis	parietal	SCAN
rs10947441	HMGA1	cis	cerebellum	SCAN
rs10947441	C6orf125	cis	cerebellum	SCAN
rs10947441	MAPK14	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33776400-33792400	Weak transcription	Right Atrium	heart
2	chr6:33781800-33792400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:33782200-33790600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:33782800-33790600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:33785400-33790200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:33787600-33790000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:33788200-33790200	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr6:33788400-33790400	Enhancers	Primary hematopoietic stem cells	blood
9	chr6:33789000-33792400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:33789200-33790200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:33789200-33790400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:33789400-33795000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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