Variant report

Variant	rs6456946
Chromosome Location	chr6:11162226-11162227
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:11154015..11156463-chr6:11160933..11163656,2	K562	blood:

Variant related genes	Relation type
ENSG00000271245	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1007741	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10601	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150561	1.00[CHB][hapmap]
rs12209631	1.00[CHB][hapmap]
rs13849	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1465131	0.85[MEX][hapmap]
rs1803710	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs1885662	0.85[MEX][hapmap]
rs2146344	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2208840	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327336	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327338	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3035	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34044517	1.00[ASN][1000 genomes]
rs4053067	0.85[MEX][hapmap]
rs4711193	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711194	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713227	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4713228	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4713229	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713247	0.84[MEX][hapmap]
rs6456968	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[MEX][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906952	1.00[CHB][hapmap]
rs6912556	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923556	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923725	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6935824	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7739880	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7746976	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7750787	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751344	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755052	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755536	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759674	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770498	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9283888	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295806	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368595	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941982	0.92[MEX][hapmap]
rs9468537	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468556	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs960944	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs960945	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[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	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6456946	C6orf105	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11145000-11172800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:11155400-11172400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:11155600-11164800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:11160200-11162400	Enhancers	HMEC	breast
5	chr6:11160400-11162400	Enhancers	NHDF-Ad	bronchial
6	chr6:11160400-11162400	Enhancers	NHEK	skin
7	chr6:11160400-11162600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:11161000-11162400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr6:11161200-11162400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr6:11161200-11162400	Enhancers	A549	lung
11	chr6:11161200-11162600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:11161200-11162600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:11161200-11162600	Enhancers	Brain Angular Gyrus	brain
14	chr6:11161200-11162800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:11161200-11162800	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr6:11161200-11162800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:11161200-11162800	Enhancers	HepG2	liver
18	chr6:11161400-11162400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:11161400-11162400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:11161400-11162400	Enhancers	HSMM	muscle
21	chr6:11161600-11162400	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr6:11161600-11162400	Enhancers	HSMMtube	muscle
23	chr6:11161800-11162600	Enhancers	Brain Anterior Caudate	brain
24	chr6:11161800-11162600	Enhancers	Brain Substantia Nigra	brain
25	chr6:11161800-11162800	Enhancers	Brain Cingulate Gyrus	brain
26	chr6:11162000-11162400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:11162000-11162400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:11162000-11162600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:11162000-11162800	Enhancers	Brain Hippocampus Middle	brain
30	chr6:11162000-11163000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:11162000-11170400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:11162000-11173000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr6:11162200-11162400	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr6:11162200-11162400	Enhancers	Esophagus	oesophagus
35	chr6:11162200-11167000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr6:11162200-11172600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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