Variant report

Variant	rs10458166
Chromosome Location	chr6:4012929-4012930
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:3257593..3260736-chr6:4009812..4013370,3	K562	blood:
2	chr6:4006763..4009757-chr6:4011766..4014574,3	K562	blood:
3	chr6:4007350..4010336-chr6:4010836..4013423,2	K562	blood:
4	chr6:4008961..4014281-chr6:4016436..4019625,9	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf146-1	chr6:4006806-4020323	NONHSAT107264

Variant related genes	Relation type
ENSG00000180822	Chromatin interaction
ENSG00000272248	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12192379	1.00[ASN][1000 genomes]
rs12210454	0.93[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921990	1.00[ASN][1000 genomes]
rs9328212	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9392027	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv1800199	chr6:3986611-4014872	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10458166	HUS1B	cis	parietal	SCAN
rs10458166	C6orf195	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:3991400-4016800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr6:3991600-4017200	Weak transcription	Fetal Brain Female	brain
3	chr6:3991600-4017400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:3991600-4017600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:3991800-4016600	Weak transcription	Aorta	Aorta
6	chr6:3991800-4017400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:3991800-4017400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:3991800-4017600	Weak transcription	Fetal Muscle Leg	muscle
9	chr6:3997400-4016200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr6:3997400-4017400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:3997600-4017600	Weak transcription	Psoas Muscle	Psoas
12	chr6:3998000-4017400	Weak transcription	NHLF	lung
13	chr6:3998200-4017400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:3998400-4016200	Weak transcription	Brain Germinal Matrix	brain
15	chr6:3998400-4017600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:3998400-4017600	Weak transcription	Small Intestine	intestine
17	chr6:3998800-4017400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr6:4000200-4017400	Weak transcription	HUVEC	blood vessel
19	chr6:4000800-4013400	Weak transcription	Placenta	Placenta
20	chr6:4001400-4016000	Weak transcription	Hela-S3	cervix
21	chr6:4004200-4013400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:4004400-4016200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr6:4005000-4016200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:4005600-4017400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr6:4007400-4013600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:4007400-4013800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:4008400-4017600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:4008600-4016200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr6:4008600-4017400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr6:4008600-4017600	Weak transcription	HSMMtube	muscle
31	chr6:4008800-4013600	Weak transcription	HSMM	muscle
32	chr6:4008800-4016200	Weak transcription	Brain Substantia Nigra	brain
33	chr6:4008800-4016200	Weak transcription	NHDF-Ad	bronchial
34	chr6:4008800-4016400	Weak transcription	Colon Smooth Muscle	Colon
35	chr6:4008800-4016600	Weak transcription	Fetal Stomach	stomach
36	chr6:4008800-4017200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr6:4008800-4017400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:4008800-4017400	Weak transcription	Brain Anterior Caudate	brain
39	chr6:4008800-4017400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr6:4008800-4017400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr6:4008800-4017400	Weak transcription	Stomach Mucosa	stomach
42	chr6:4008800-4017400	Weak transcription	A549	lung
43	chr6:4009000-4013600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:4009000-4014400	Weak transcription	Fetal Intestine Large	intestine
45	chr6:4009000-4017400	Weak transcription	NH-A	brain
46	chr6:4009000-4017400	Weak transcription	Osteobl	bone
47	chr6:4009800-4013000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:4010000-4015200	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr6:4010400-4016400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr6:4011000-4013000	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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