Variant report

Variant	rs17141053
Chromosome Location	chr7:117854471-117854472
allele	C/T
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	POLR2A	chr7:117854189-117854975	U87	brain:	n/a	n/a
2	POLR2A	chr7:117854377-117854787	GM12878	blood:	n/a	n/a
3	POLR2A	chr7:117854285-117854945	HUVEC	blood vessel:	n/a	n/a
4	E2F6	chr7:117854148-117854908	A549	lung:	n/a	chr7:117854688-117854697
5	POLR2A	chr7:117854284-117854959	A549	lung:	n/a	n/a
6	POLR2A	chr7:117854356-117854938	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr7:117854335-117854931	GM12878	blood:	n/a	n/a
8	TAF1	chr7:117854415-117854912	SK-N-SH	brain:	n/a	n/a
9	YY1	chr7:117854076-117854937	SK-N-SH_RA	brain:	n/a	n/a
10	MAX	chr7:117854001-117854977	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr7:117854366-117854931	A549	lung:	n/a	n/a
12	RELA	chr7:117854265-117854971	GM19099	blood:	n/a	n/a
13	POLR2A	chr7:117854317-117854958	GM12892	blood:	n/a	n/a
14	POLR2A	chr7:117854372-117854969	U87	brain:	n/a	n/a
15	POLR2A	chr7:117854193-117854984	GM12891	blood:	n/a	n/a
16	POLR2A	chr7:117854336-117854895	HUVEC	blood vessel:	n/a	n/a
17	MAX	chr7:117854056-117855059	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr7:117854237-117854901	HUVEC	blood vessel:	n/a	n/a
19	YY1	chr7:117854069-117854922	SK-N-SH_RA	brain:	n/a	n/a
20	POLR2A	chr7:117854410-117854677	GM12892	blood:	n/a	n/a
21	POLR2A	chr7:117854254-117854943	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr7:117854172-117854968	GM12892	blood:	n/a	n/a
23	POLR2A	chr7:117854322-117854992	GM18526	blood:	n/a	n/a
24	MAX	chr7:117853996-117855041	A549	lung:	n/a	n/a
25	REST	chr7:117854323-117854647	SK-N-SH	brain:	n/a	chr7:117854469-117854478
26	POLR2A	chr7:117854208-117854954	GM15510	blood:	n/a	n/a
27	POLR2A	chr7:117854392-117854720	MCF-7	breast:	n/a	n/a
28	POLR2A	chr7:117854217-117855035	SK-N-MC	brain:	n/a	n/a
29	MAX	chr7:117854137-117854952	A549	lung:	n/a	n/a
30	POLR2A	chr7:117854404-117854903	GM12878	blood:	n/a	n/a
31	POLR2A	chr7:117854270-117855008	HEK293	kidney:	n/a	n/a
32	TCF7L2	chr7:117854306-117854752	PANC-1	pancreas:	n/a	n/a
33	MXI1	chr7:117854004-117854816	IMR90	lung:	n/a	n/a
34	POLR2A	chr7:117854424-117854671	GM12891	blood:	n/a	n/a
35	POLR2A	chr7:117854249-117855147	PFSK-1	brain:	n/a	n/a
36	POLR2A	chr7:117854231-117854999	SK-N-SH	brain:	n/a	n/a
37	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
38	POLR2A	chr7:117854317-117854876	U87	brain:	n/a	n/a
39	POLR2A	chr7:117854361-117855043	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr7:117854367-117854857	GM12892	blood:	n/a	n/a
41	POLR2A	chr7:117854233-117854880	GM12892	blood:	n/a	n/a
42	POLR2A	chr7:117854464-117854815	GM12878	blood:	n/a	n/a
43	POLR2A	chr7:117854433-117854859	A549	lung:	n/a	n/a
44	POLR2A	chr7:117854127-117854955	GM18505	blood:	n/a	n/a
45	YY1	chr7:117854385-117854798	GM12878	blood:	n/a	n/a
46	POLR2A	chr7:117854381-117854847	PANC-1	pancreas:	n/a	n/a
47	POLR2A	chr7:117854142-117855005	Raji	blood:	n/a	n/a
48	POLR2A	chr7:117854453-117854831	A549	lung:	n/a	n/a
49	POLR2A	chr7:117854357-117854894	ProgFib	skin:	n/a	n/a
50	POLR2A	chr7:117854094-117855027	Gliobla	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:117822159..117825807-chr7:117854196..117858736,4	K562	blood:

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

Extended variants
information (count: 53 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1015782	0.83[EUR][1000 genomes]
rs10247768	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10487392	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11487110	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs11542074	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11974039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11983651	0.96[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs12154684	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1544583	0.90[EUR][1000 genomes]
rs1544584	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17140984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2041527	0.81[CEU][hapmap]
rs2058418	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs2215628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2286863	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2286865	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs28260	0.82[EUR][1000 genomes]
rs33924981	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34010516	0.90[EUR][1000 genomes]
rs34019303	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35218902	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35485182	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41903	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41904	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41912	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41921	0.84[EUR][1000 genomes]
rs41923	0.85[EUR][1000 genomes]
rs41924	0.85[EUR][1000 genomes]
rs41925	0.82[EUR][1000 genomes]
rs41930	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41931	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41936	0.85[EUR][1000 genomes]
rs41962	0.81[EUR][1000 genomes]
rs41989	0.81[EUR][1000 genomes]
rs45604739	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4730837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5002232	0.81[EUR][1000 genomes]
rs57308869	0.82[ASN][1000 genomes]
rs62466471	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62466515	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62468297	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62469806	0.91[EUR][1000 genomes]
rs6466648	0.83[EUR][1000 genomes]
rs6942513	0.84[CEU][hapmap]
rs6960940	0.82[EUR][1000 genomes]
rs769435	0.84[CEU][hapmap]
rs7786233	0.92[CEU][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7801976	0.85[EUR][1000 genomes]
rs9641593	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9656259	0.83[EUR][1000 genomes]
rs992035	0.84[CEU][hapmap]

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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17141053	NAA38	cis	parietal	SCAN
rs17141053	ANKRD7	cis	cerebellum	SCAN
rs17141053	LSM8	cis	multi-tissue	Pritchard
rs17141053	ANKRD7	cis	parietal	SCAN
rs17141053	KCND2	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117854000-117854600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr7:117854000-117854600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr7:117854000-117854600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr7:117854000-117854600	Flanking Active TSS	Fetal Muscle Trunk	muscle
5	chr7:117854000-117854600	Flanking Active TSS	Fetal Thymus	thymus
6	chr7:117854000-117854600	Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr7:117854000-117854600	Active TSS	Thymus	Thymus
8	chr7:117854000-117854600	Flanking Active TSS	GM12878-XiMat	blood
9	chr7:117854000-117854600	Active TSS	HMEC	breast
10	chr7:117854000-117854600	Flanking Active TSS	NHEK	skin
11	chr7:117854000-117854800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
12	chr7:117854000-117854800	Active TSS	Brain Substantia Nigra	brain
13	chr7:117854000-117854800	Active TSS	Rectal Smooth Muscle	rectum
14	chr7:117854000-117854800	Active TSS	Stomach Mucosa	stomach
15	chr7:117854000-117854800	Active TSS	Osteobl	bone
16	chr7:117854000-117855000	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr7:117854000-117855000	Flanking Active TSS	Primary B cells from peripheral blood	blood
18	chr7:117854000-117855000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
19	chr7:117854000-117855000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr7:117854000-117855000	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
21	chr7:117854000-117855000	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr7:117854000-117855000	Active TSS	Aorta	Aorta
23	chr7:117854000-117855000	Active TSS	Brain Cingulate Gyrus	brain
24	chr7:117854000-117855000	Active TSS	Colonic Mucosa	Colon
25	chr7:117854000-117855000	Active TSS	Fetal Brain Male	brain
26	chr7:117854000-117855000	Active TSS	Fetal Heart	heart
27	chr7:117854000-117855000	Flanking Active TSS	Placenta	Placenta
28	chr7:117854000-117855000	Active TSS	Placenta Amnion	Placenta Amnion
29	chr7:117854000-117855000	Active TSS	Right Ventricle	heart
30	chr7:117854000-117855000	Active TSS	A549	lung
31	chr7:117854000-117855200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:117854000-117855200	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr7:117854000-117855200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr7:117854000-117855200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr7:117854000-117855200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr7:117854000-117855200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr7:117854000-117855200	Active TSS	Brain Angular Gyrus	brain
38	chr7:117854000-117855200	Active TSS	Brain Anterior Caudate	brain
39	chr7:117854000-117855200	Active TSS	Brain Germinal Matrix	brain
40	chr7:117854000-117855200	Active TSS	Brain Hippocampus Middle	brain
41	chr7:117854000-117855200	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr7:117854000-117855200	Active TSS	Fetal Brain Female	brain
43	chr7:117854000-117855200	Active TSS	Fetal Intestine Large	intestine
44	chr7:117854000-117855200	Active TSS	Fetal Intestine Small	intestine
45	chr7:117854000-117855200	Active TSS	Fetal Kidney	kidney
46	chr7:117854000-117855200	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr7:117854000-117855200	Active TSS	Fetal Stomach	stomach
48	chr7:117854000-117855200	Active TSS	Psoas Muscle	Psoas
49	chr7:117854000-117855200	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr7:117854000-117855200	Active TSS	Right Atrium	heart

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