Variant report

Variant	rs12665401
Chromosome Location	chr6:29717380-29717381
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr6:29716018-29717456	K562	blood:	n/a	chr6:29716903-29716913
2	POLR2A	chr6:29717202-29717401	ProgFib	skin:	n/a	n/a
3	POLR2A	chr6:29716473-29717834	PFSK-1	brain:	n/a	n/a
4	BHLHE40	chr6:29716713-29717497	GM12878	blood:	n/a	n/a
5	SIN3A	chr6:29715713-29717573	H1-hESC	embryonic stem cell:	n/a	chr6:29717251-29717262 chr6:29717074-29717085
6	ELK1	chr6:29717215-29717413	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:29715691-29717474	K562	blood:	n/a	n/a
8	RELA	chr6:29716550-29717846	GM15510	blood:	n/a	n/a
9	MAFK	chr6:29717219-29717419	HepG2	liver:	n/a	n/a
10	POLR2A	chr6:29716547-29717491	GM18505	blood:	n/a	n/a
11	MAX	chr6:29716411-29717386	H1-hESC	embryonic stem cell:	n/a	chr6:29716903-29716913
12	JUND	chr6:29717270-29717830	K562	blood:	n/a	chr6:29717659-29717668
13	POLR2A	chr6:29716467-29717391	Hela-S3	cervix:	n/a	n/a
14	BHLHE40	chr6:29717317-29717394	K562	blood:	n/a	n/a
15	HCFC1	chr6:29716302-29717779	K562	blood:	n/a	n/a
16	POLR2A	chr6:29716603-29717501	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:29717368-29717418	PFSK-1	brain:	n/a
2	chr6:29717368-29717418	HMEC	breast:	n/a
3	chr6:29717368-29717418	GM19239	blood:	n/a
4	chr6:29717368-29717418	HNPCEpiC	eye:	n/a
5	chr6:29717368-29717418	AG04450	lung:	fetal
6	chr6:29717368-29717418	LNCaP	prostate:	n/a
7	chr6:29717368-29717418	HEEpiC	esophagus:	n/a
8	chr6:29717368-29717418	MCF-7	breast:	n/a
9	chr6:29717368-29717418	MCF10A-Er-Src	breast:	n/a
10	chr6:29717368-29717418	T-47D	breast:	n/a
11	chr6:29717368-29717418	HPAEpiC	pulmonary alveolar:	n/a
12	chr6:29717368-29717418	ProgFib	skin:	n/a
13	chr6:29717368-29717418	Jurkat	blood:	n/a
14	chr6:29717368-29717418	GM12878	blood:	n/a
15	chr6:29717368-29717418	RPTEC	kidney:	n/a
16	chr6:29717368-29717418	AG09319	gingival:	n/a
17	chr6:29717368-29717418	NHBE	bronchial:	n/a
18	chr6:29717368-29717418	GM12892	blood:	n/a
19	chr6:29717368-29717418	PANC-1	pancreas:	n/a
20	chr6:29717368-29717418	HUVEC	blood vessel:	n/a
21	chr6:29717368-29717418	GM12891	blood:	n/a
22	chr6:29717368-29717418	GM06990	blood:	n/a
23	chr6:29717368-29717418	IMR90	lung:	fetal
24	chr6:29717368-29717418	PrEC	prostate:	n/a
25	chr6:29717368-29717418	HIPEpiC	eye:	n/a
26	chr6:29717368-29717418	SK-N-SH_RA	brain:	n/a
27	chr6:29717368-29717418	NT2-D1	testis:	n/a
28	chr6:29717368-29717418	SK-N-SH	brain:	n/a
29	chr6:29717368-29717418	ovcar-3	ovarian:	n/a
30	chr6:29717368-29717418	HCM	heart:	n/a
31	chr6:29717368-29717418	SKMC	muscle:	n/a
32	chr6:29717368-29717418	HL-60	blood:	n/a
33	chr6:29717368-29717418	NH-A	brain:	n/a
34	chr6:29717368-29717418	BE2_C	brain:	n/a
35	chr6:29717368-29717418	BJ	skin:	n/a
36	chr6:29717368-29717418	NB4	blood:	n/a
37	chr6:29717368-29717418	SK-N-MC	brain:	n/a
38	chr6:29717368-29717418	HCF	heart:	n/a
39	chr6:29717368-29717418	SAEC	small airway:	n/a
40	chr6:29717368-29717418	AG10803	skin:	n/a
41	chr6:29717368-29717418	HRPEpiC	eye:	n/a
42	chr6:29717368-29717418	Hela-S3	cervix:	n/a
43	chr6:29717368-29717418	A549	lung:	n/a
44	chr6:29717368-29717418	NHDF-neo	bronchial:	n/a
45	chr6:29717368-29717418	HCT-116	colon:	n/a
46	chr6:29717368-29717418	Hepatocyte	liver:	n/a
47	chr6:29717368-29717418	HCPEpiC	choroid plexus:	n/a
48	chr6:29717368-29717418	H1-hESC	embryonic stem cell:	embryo
49	chr6:29717368-29717418	HEK293	kidney:	embryo
50	chr6:29717368-29717418	Caco-2	colon:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29716316..29718223-chr6:29719581..29721724,2	MCF-7	breast:

No data

Variant related genes	Relation type
MICE	TF binding region
ENSG00000199290	TF binding region
HLA-F-AS1	TF binding region
ENSG00000199290	CpG island
HLA-F-AS1	CpG island
MICE	CpG island
ENSG00000272236	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs16867712	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2394164	0.94[AFR][1000 genomes]
rs34260811	0.81[AFR][1000 genomes]
rs4713240	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4713242	0.94[AFR][1000 genomes]
rs4713243	0.81[EUR][1000 genomes]
rs4713244	0.81[AMR][1000 genomes]
rs7759474	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7759482	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9368609	0.94[AFR][1000 genomes]
rs9391660	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	esv1821077	chr6:29670915-29726207	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv10809	chr6:29692573-29794119	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv883532	chr6:29703262-29814963	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv883534	chr6:29708222-29724310	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	esv3441842	chr6:29715749-29942950	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	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
rs12665401	HLA-A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29715400-29717400	Active TSS	H9 Cell Line	embryonic stem cell
2	chr6:29715400-29717600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr6:29715400-29717800	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr6:29715600-29717400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr6:29715600-29718000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr6:29715800-29717400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
7	chr6:29715800-29717400	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr6:29715800-29717600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:29715800-29717600	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr6:29715800-29717600	Bivalent/Poised TSS	Fetal Lung	lung
11	chr6:29716000-29717400	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr6:29716000-29717400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr6:29716000-29717400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:29716000-29717400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
15	chr6:29716000-29717400	Bivalent/Poised TSS	Fetal Brain Female	brain
16	chr6:29716000-29717400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
17	chr6:29716000-29717400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
18	chr6:29716000-29717400	Flanking Bivalent TSS/Enh	Placenta	Placenta
19	chr6:29716000-29717400	Flanking Active TSS	HUVEC	blood vessel
20	chr6:29716000-29717600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:29716000-29717600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
22	chr6:29716000-29717600	Active TSS	Primary T cells from cord blood	blood
23	chr6:29716000-29717800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:29716200-29717400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:29716200-29717400	Active TSS	Brain Angular Gyrus	brain
26	chr6:29716200-29717400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
27	chr6:29716200-29717400	Active TSS	Ovary	ovary
28	chr6:29716200-29717400	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr6:29716200-29717600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:29716200-29717600	Active TSS	Hela-S3	cervix
31	chr6:29716400-29717600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:29716400-29717800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:29716800-29717400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:29716800-29717600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr6:29716800-29717600	Active TSS	Colonic Mucosa	Colon
36	chr6:29716800-29717800	Enhancers	Placenta Amnion	Placenta Amnion
37	chr6:29717000-29717400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:29717000-29717400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr6:29717000-29717400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr6:29717000-29717400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:29717000-29717400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr6:29717000-29717400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:29717000-29717400	Flanking Bivalent TSS/Enh	Thymus	Thymus
44	chr6:29717000-29717600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
45	chr6:29717000-29717600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr6:29717000-29717600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:29717000-29717600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:29717000-29717600	Flanking Bivalent TSS/Enh	HepG2	liver
49	chr6:29717000-29717600	Flanking Active TSS	HMEC	breast
50	chr6:29717000-29717800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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