Variant report

Variant	rs12665339
Chromosome Location	chr6:30601232-30601233
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr6:30601180-30601292	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:30601190-30601275	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:30601203-30601263	A549	lung:	n/a	n/a
4	HEY1	chr6:30601075-30601367	HepG2	liver:	n/a	n/a
5	POLR2A	chr6:30601156-30601277	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:30601195-30601276	A549	lung:	n/a	n/a
7	POLR2A	chr6:30601036-30601398	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:30601190-30601275	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30455831..30458376-chr6:30599698..30601458,2	MCF-7	breast:
2	chr6:30581846..30586345-chr6:30599769..30603372,4	MCF-7	breast:
3	chr6:30598934..30603301-chr6:30608761..30613584,7	MCF-7	breast:

Variant related genes	Relation type
PTMAP1	TF binding region
ENSG00000204592	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000137343	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000204569	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12174151	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2252745	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
4	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
5	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
6	nsv884086	chr6:30462084-30672757	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	798 gene(s)	inside rSNPs	diseases
7	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12665339	CCHCR1	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30593600-30613800	Weak transcription	Hela-S3	cervix
2	chr6:30595200-30607000	Weak transcription	Right Atrium	heart
3	chr6:30595200-30609000	Weak transcription	Colonic Mucosa	Colon
4	chr6:30595400-30601400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr6:30595400-30607800	Weak transcription	Right Ventricle	heart
6	chr6:30595400-30608200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr6:30595400-30608400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:30595400-30614000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:30595400-30614800	Weak transcription	Small Intestine	intestine
10	chr6:30595600-30601400	Weak transcription	NH-A	brain
11	chr6:30595600-30605200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:30595600-30608000	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr6:30595600-30608200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:30595600-30608600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr6:30595600-30611000	Weak transcription	Primary B cells from cord blood	blood
16	chr6:30595600-30613000	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:30595600-30613800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr6:30595600-30614200	Strong transcription	Fetal Muscle Trunk	muscle
19	chr6:30595600-30614200	Strong transcription	Fetal Stomach	stomach
20	chr6:30595600-30614200	Weak transcription	Psoas Muscle	Psoas
21	chr6:30595600-30614400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr6:30595800-30601800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:30595800-30602000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:30595800-30602000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:30595800-30602000	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr6:30595800-30602200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:30595800-30602400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr6:30595800-30602400	Strong transcription	Fetal Intestine Large	intestine
29	chr6:30595800-30602400	Strong transcription	Fetal Thymus	thymus
30	chr6:30595800-30603200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:30595800-30604200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr6:30595800-30608200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr6:30595800-30608800	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr6:30595800-30613000	Strong transcription	Fetal Lung	lung
35	chr6:30595800-30613600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:30595800-30613600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr6:30595800-30614000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:30595800-30614200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:30596000-30601800	Strong transcription	Ovary	ovary
40	chr6:30596000-30602000	Strong transcription	Brain Anterior Caudate	brain
41	chr6:30596000-30602000	Strong transcription	Brain Cingulate Gyrus	brain
42	chr6:30596000-30602000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr6:30596000-30602400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr6:30596000-30602400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:30596000-30602800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:30596000-30604200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr6:30596000-30605200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:30596000-30605400	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr6:30596000-30605800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:30596000-30613800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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