Variant report

Variant	rs12669395
Chromosome Location	chr7:117854329-117854330
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:35)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:35 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:117854189-117854975	U87	brain:	n/a	n/a
2	POLR2A	chr7:117854285-117854945	HUVEC	blood vessel:	n/a	n/a
3	E2F6	chr7:117854148-117854908	A549	lung:	n/a	chr7:117854688-117854697
4	POLR2A	chr7:117854284-117854959	A549	lung:	n/a	n/a
5	YY1	chr7:117854076-117854937	SK-N-SH_RA	brain:	n/a	n/a
6	MAX	chr7:117854001-117854977	SK-N-SH	brain:	n/a	n/a
7	RELA	chr7:117854265-117854971	GM19099	blood:	n/a	n/a
8	POLR2A	chr7:117854317-117854958	GM12892	blood:	n/a	n/a
9	POLR2A	chr7:117854193-117854984	GM12891	blood:	n/a	n/a
10	MAX	chr7:117854056-117855059	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr7:117854237-117854901	HUVEC	blood vessel:	n/a	n/a
12	YY1	chr7:117854069-117854922	SK-N-SH_RA	brain:	n/a	n/a
13	POLR2A	chr7:117854254-117854943	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr7:117854172-117854968	GM12892	blood:	n/a	n/a
15	POLR2A	chr7:117854322-117854992	GM18526	blood:	n/a	n/a
16	MAX	chr7:117853996-117855041	A549	lung:	n/a	n/a
17	REST	chr7:117854323-117854647	SK-N-SH	brain:	n/a	chr7:117854469-117854478
18	POLR2A	chr7:117854208-117854954	GM15510	blood:	n/a	n/a
19	POLR2A	chr7:117854217-117855035	SK-N-MC	brain:	n/a	n/a
20	MAX	chr7:117854137-117854952	A549	lung:	n/a	n/a
21	POLR2A	chr7:117854270-117855008	HEK293	kidney:	n/a	n/a
22	TCF7L2	chr7:117854306-117854752	PANC-1	pancreas:	n/a	n/a
23	MXI1	chr7:117854004-117854816	IMR90	lung:	n/a	n/a
24	POLR2A	chr7:117854249-117855147	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr7:117854231-117854999	SK-N-SH	brain:	n/a	n/a
26	NRF1	chr7:117854013-117855543	SK-N-SH	brain:	n/a	chr7:117854689-117854698 chr7:117854684-117854698 chr7:117854687-117854696 chr7:117854687-117854698 chr7:117854687-117854701
27	POLR2A	chr7:117854317-117854876	U87	brain:	n/a	n/a
28	POLR2A	chr7:117854233-117854880	GM12892	blood:	n/a	n/a
29	POLR2A	chr7:117854127-117854955	GM18505	blood:	n/a	n/a
30	POLR2A	chr7:117854142-117855005	Raji	blood:	n/a	n/a
31	POLR2A	chr7:117854094-117855027	Gliobla	brain:	n/a	n/a
32	EBF1	chr7:117854229-117854599	GM12878	blood:	n/a	chr7:117854446-117854455 chr7:117854446-117854456
33	POLR2A	chr7:117854159-117854975	GM18951	blood:	n/a	n/a
34	POLR2A	chr7:117854210-117854995	GM19099	blood:	n/a	n/a
35	POLR2A	chr7:117854298-117854953	GM19193	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:117854304-117854354	HMEC	breast:	n/a
2	chr7:117854304-117854354	HepG2	liver:	n/a
3	chr7:117854304-117854354	NHBE	bronchial:	n/a
4	chr7:117854304-117854354	A549	lung:	n/a
5	chr7:117854304-117854354	HRCEpiC	kidney:	n/a
6	chr7:117854304-117854354	HEK293	kidney:	embryo
7	chr7:117854304-117854354	PANC-1	pancreas:	n/a
8	chr7:117854304-117854354	Hela-S3	cervix:	n/a
9	chr7:117854304-117854354	AoSMC	blood vessel:	n/a
10	chr7:117854304-117854354	H1-hESC	embryonic stem cell:	embryo
11	chr7:117854304-117854354	HAEpiC	amniotic membrane:	n/a
12	chr7:117854304-117854354	SK-N-SH	brain:	n/a
13	chr7:117854304-117854354	PrEC	prostate:	n/a
14	chr7:117854304-117854354	NH-A	brain:	n/a
15	chr7:117854304-117854354	T-47D	breast:	n/a
16	chr7:117854304-117854354	LNCaP	prostate:	n/a
17	chr7:117854304-117854354	HEEpiC	esophagus:	n/a
18	chr7:117854304-117854354	MCF10A-Er-Src	breast:	n/a
19	chr7:117854304-117854354	SKMC	muscle:	n/a
20	chr7:117854304-117854354	SK-N-MC	brain:	n/a
21	chr7:117854304-117854354	Caco-2	colon:	n/a
22	chr7:117854304-117854354	HCT-116	colon:	n/a
23	chr7:117854304-117854354	ovcar-3	ovarian:	n/a
24	chr7:117854304-117854354	AG09319	gingival:	n/a
25	chr7:117854304-117854354	AG04449	skin:	fetal
26	chr7:117854304-117854354	HIPEpiC	eye:	n/a
27	chr7:117854304-117854354	AG04450	lung:	fetal
28	chr7:117854304-117854354	AG09309	skin:	n/a
29	chr7:117854304-117854354	GM12891	blood:	n/a
30	chr7:117854304-117854354	RPTEC	kidney:	n/a
31	chr7:117854304-117854354	NB4	blood:	n/a
32	chr7:117854304-117854354	PFSK-1	brain:	n/a
33	chr7:117854304-117854354	HCPEpiC	choroid plexus:	n/a
34	chr7:117854304-117854354	GM19239	blood:	n/a
35	chr7:117854304-117854354	BJ	skin:	n/a
36	chr7:117854304-117854354	ECC-1	luminal epithelium:	n/a
37	chr7:117854304-117854354	Jurkat	blood:	n/a
38	chr7:117854304-117854354	NHDF-neo	bronchial:	n/a
39	chr7:117854304-117854354	AG10803	skin:	n/a
40	chr7:117854304-117854354	HRE	kidney:	n/a
41	chr7:117854304-117854354	HUVEC	blood vessel:	n/a
42	chr7:117854304-117854354	K562	blood:	n/a
43	chr7:117854304-117854354	GM12892	blood:	n/a
44	chr7:117854304-117854354	HL-60	blood:	n/a
45	chr7:117854304-117854354	HCM	heart:	n/a
46	chr7:117854304-117854354	Hepatocyte	liver:	n/a
47	chr7:117854304-117854354	SK-N-SH_RA	brain:	n/a
48	chr7:117854304-117854354	GM12878	blood:	n/a
49	chr7:117854304-117854354	ProgFib	skin:	n/a
50	chr7:117854304-117854354	SAEC	small airway:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:117822159..117825807-chr7:117854196..117858736,4	K562	blood:
2	chr7:117851686..117854331-chr7:117855579..117858134,2	K562	blood:
3	chr7:117851576..117854331-chr7:117855447..117858134,2	K562	blood:

No data

Variant related genes	Relation type
ANKRD7	TF binding region
ANKRD7	CpG island
ENSG00000128534	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10215186	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10235876	0.82[ASN][1000 genomes]
rs10953865	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10953866	0.90[EUR][1000 genomes]
rs11981239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11982333	0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12674239	0.87[EUR][1000 genomes]
rs17140846	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17141130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17141139	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17141216	0.90[EUR][1000 genomes]
rs17141219	0.90[EUR][1000 genomes]
rs17141231	0.90[EUR][1000 genomes]
rs17141244	0.90[EUR][1000 genomes]
rs34126707	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3757800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4454229	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57970913	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58836778	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59338276	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59768076	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60680906	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61632875	0.90[EUR][1000 genomes]
rs6948367	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6959973	0.90[EUR][1000 genomes]
rs6973741	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73483487	0.90[EUR][1000 genomes]
rs73716919	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73716927	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73716929	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73716958	0.86[EUR][1000 genomes]
rs973023	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.88[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	nsv869971	chr7:117420583-118274149	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv889088	chr7:117744660-117913648	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117854000-117854400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr7:117854000-117854400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr7:117854000-117854400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr7:117854000-117854400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr7:117854000-117854400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
6	chr7:117854000-117854400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
7	chr7:117854000-117854400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:117854000-117854400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr7:117854000-117854400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr7:117854000-117854400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr7:117854000-117854400	Flanking Active TSS	Duodenum Mucosa	Duodenum
12	chr7:117854000-117854400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr7:117854000-117854400	Flanking Active TSS	Esophagus	oesophagus
14	chr7:117854000-117854400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
15	chr7:117854000-117854400	Flanking Active TSS	Fetal Muscle Leg	muscle
16	chr7:117854000-117854400	Flanking Active TSS	Left Ventricle	heart
17	chr7:117854000-117854400	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr7:117854000-117854400	Flanking Active TSS	Dnd41	blood
19	chr7:117854000-117854400	Flanking Active TSS	NHDF-Ad	bronchial
20	chr7:117854000-117854600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr7:117854000-117854600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr7:117854000-117854600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr7:117854000-117854600	Flanking Active TSS	Fetal Muscle Trunk	muscle
24	chr7:117854000-117854600	Flanking Active TSS	Fetal Thymus	thymus
25	chr7:117854000-117854600	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr7:117854000-117854600	Active TSS	Thymus	Thymus
27	chr7:117854000-117854600	Flanking Active TSS	GM12878-XiMat	blood
28	chr7:117854000-117854600	Active TSS	HMEC	breast
29	chr7:117854000-117854600	Flanking Active TSS	NHEK	skin
30	chr7:117854000-117854800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:117854000-117854800	Active TSS	Brain Substantia Nigra	brain
32	chr7:117854000-117854800	Active TSS	Rectal Smooth Muscle	rectum
33	chr7:117854000-117854800	Active TSS	Stomach Mucosa	stomach
34	chr7:117854000-117854800	Active TSS	Osteobl	bone
35	chr7:117854000-117855000	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr7:117854000-117855000	Flanking Active TSS	Primary B cells from peripheral blood	blood
37	chr7:117854000-117855000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
38	chr7:117854000-117855000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr7:117854000-117855000	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
40	chr7:117854000-117855000	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr7:117854000-117855000	Active TSS	Aorta	Aorta
42	chr7:117854000-117855000	Active TSS	Brain Cingulate Gyrus	brain
43	chr7:117854000-117855000	Active TSS	Colonic Mucosa	Colon
44	chr7:117854000-117855000	Active TSS	Fetal Brain Male	brain
45	chr7:117854000-117855000	Active TSS	Fetal Heart	heart
46	chr7:117854000-117855000	Flanking Active TSS	Placenta	Placenta
47	chr7:117854000-117855000	Active TSS	Placenta Amnion	Placenta Amnion
48	chr7:117854000-117855000	Active TSS	Right Ventricle	heart
49	chr7:117854000-117855000	Active TSS	A549	lung
50	chr7:117854000-117855200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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