Variant report

Variant	rs1046279
Chromosome Location	chr6:36932571-36932572
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36930754..36936310-chr6:36950773..36956274,7	MCF-7	breast:
2	chr6:36929829..36933522-chr6:36953197..36956380,5	MCF-7	breast:
3	chr6:36928176..36930778-chr6:36931482..36933887,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164530	Chromatin interaction
ENSG00000137409	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1063021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150786	0.87[CHB][hapmap]
rs1405069	0.81[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs16889316	0.86[CHB][hapmap]
rs2296934	0.87[CHB][hapmap];0.84[CHD][hapmap]
rs4147297	0.81[JPT][hapmap]
rs4714025	0.82[CHB][hapmap]
rs707542	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs707998	0.87[CHB][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	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv885815	chr6:36915906-36979583	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1046279	C6orf126	cis	cerebellum	SCAN
rs1046279	C6orf1	cis	parietal	SCAN
rs1046279	CDKN1A	cis	cerebellum	SCAN
rs1046279	PI16	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36927200-36933400	Enhancers	Stomach Mucosa	stomach
2	chr6:36927800-36933200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:36928000-36933600	Enhancers	Primary T cells fromperipheralblood	blood
4	chr6:36928200-36935200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:36928600-36935000	Weak transcription	HSMMtube	muscle
6	chr6:36928600-36935400	Weak transcription	Small Intestine	intestine
7	chr6:36928800-36934000	Weak transcription	HSMM	muscle
8	chr6:36928800-36935000	Weak transcription	HUVEC	blood vessel
9	chr6:36929000-36934200	Weak transcription	Osteobl	bone
10	chr6:36929000-36934400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:36929000-36934800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:36929000-36935200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr6:36929000-36935400	Weak transcription	Ovary	ovary
14	chr6:36929000-36935400	Weak transcription	A549	lung
15	chr6:36929200-36934600	Weak transcription	NH-A	brain
16	chr6:36929400-36934400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:36929400-36935200	Weak transcription	K562	blood
18	chr6:36929600-36936800	Weak transcription	Hela-S3	cervix
19	chr6:36929800-36933200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:36930000-36933000	Enhancers	Primary B cells from cord blood	blood
21	chr6:36930400-36933000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr6:36930400-36933200	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr6:36930600-36933000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr6:36930600-36933000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:36930600-36933000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:36930600-36933000	Enhancers	Dnd41	blood
27	chr6:36930600-36933200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:36930600-36933200	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr6:36930600-36933200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:36930600-36933200	Enhancers	Fetal Heart	heart
31	chr6:36930800-36932600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr6:36930800-36933200	Enhancers	Primary hematopoietic stem cells	blood
33	chr6:36930800-36933200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr6:36931000-36932600	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr6:36931000-36932600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:36931000-36932600	Enhancers	Brain Substantia Nigra	brain
37	chr6:36931000-36932600	Enhancers	Esophagus	oesophagus
38	chr6:36931000-36933000	Enhancers	Brain Anterior Caudate	brain
39	chr6:36931000-36933200	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr6:36931000-36933200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr6:36931000-36933200	Enhancers	Right Ventricle	heart
42	chr6:36931200-36932600	Enhancers	Brain Hippocampus Middle	brain
43	chr6:36931200-36932600	Enhancers	Fetal Muscle Leg	muscle
44	chr6:36931200-36933000	Enhancers	Primary B cells from peripheral blood	blood
45	chr6:36931200-36933000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:36931200-36933200	Enhancers	Duodenum Mucosa	Duodenum
47	chr6:36931200-36933200	Enhancers	Gastric	stomach
48	chr6:36931200-36933200	Enhancers	Left Ventricle	heart
49	chr6:36931200-36933200	Enhancers	Pancreas	Pancrea
50	chr6:36931200-36933200	Enhancers	Skeletal Muscle Female	skeletal muscle

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