Variant report

Variant	rs2540169
Chromosome Location	chr1:156218114-156218115
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:65)
CpG islands
(count:122)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:65 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:156215890-156218252	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr1:156216400-156218293	K562	blood:	n/a	n/a
3	POLR2A	chr1:156215498-156218434	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr1:156215881-156218325	K562	blood:	n/a	n/a
5	POLR2A	chr1:156217863-156218215	HUVEC	blood vessel:	n/a	n/a
6	ZNF263	chr1:156216958-156218159	HEK293-T-REx	kidney:	n/a	chr1:156217566-156217575
7	POLR2A	chr1:156216492-156218234	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr1:156216799-156218289	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:156215772-156218296	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:156215146-156218463	GM12892	blood:	n/a	n/a
11	NFATC1	chr1:156217643-156218317	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:156216338-156218332	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr1:156214846-156218301	GM12891	blood:	n/a	n/a
14	POLR2A	chr1:156216251-156218314	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr1:156217923-156218296	GM12891	blood:	n/a	n/a
16	POLR2A	chr1:156216801-156218374	HCT-116	colon:	n/a	n/a
17	POLR2A	chr1:156216226-156218307	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:156217304-156218301	K562	blood:	n/a	n/a
19	POLR2A	chr1:156210570-156218256	HepG2	liver:	n/a	n/a
20	POLR2A	chr1:156215112-156218443	HL-60	blood:	n/a	n/a
21	POLR2A	chr1:156217676-156218259	HepG2	liver:	n/a	n/a
22	POLR2A	chr1:156217247-156218143	NB4	blood:	n/a	n/a
23	POLR2A	chr1:156215087-156218226	A549	lung:	n/a	n/a
24	PML	chr1:156216869-156218343	GM12878	blood:	n/a	chr1:156218161-156218169
25	POLR2A	chr1:156216863-156218249	GM18505	blood:	n/a	n/a
26	POLR2A	chr1:156216309-156218289	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr1:156217912-156218155	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr1:156214929-156218421	GM12891	blood:	n/a	n/a
29	FOSL2	chr1:156216446-156218295	HepG2	liver:	n/a	chr1:156217172-156217181
30	POLR2A	chr1:156217134-156218120	GM18951	blood:	n/a	n/a
31	POLR2A	chr1:156217818-156218226	H1-neurons	neurons:	n/a	n/a
32	POLR2A	chr1:156215549-156218304	K562	blood:	n/a	n/a
33	POLR2A	chr1:156215612-156218269	MCF-7	breast:	n/a	n/a
34	POLR2A	chr1:156215747-156218303	PFSK-1	brain:	n/a	n/a
35	POLR2A	chr1:156215867-156220677	SK-N-MC	brain:	n/a	n/a
36	POLR2A	chr1:156214890-156219401	HepG2	liver:	n/a	n/a
37	POLR2A	chr1:156216564-156218242	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr1:156218002-156218163	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr1:156214626-156218406	GM12892	blood:	n/a	n/a
40	POLR2A	chr1:156215260-156218257	GM19193	blood:	n/a	n/a
41	NFATC1	chr1:156216878-156218294	GM12878	blood:	n/a	n/a
42	POLR2A	chr1:156216864-156218375	HCT-116	colon:	n/a	n/a
43	POLR2A	chr1:156215214-156218284	PANC-1	pancreas:	n/a	n/a
44	POLR2A	chr1:156215064-156218295	GM12891	blood:	n/a	n/a
45	POLR2A	chr1:156216168-156218347	GM12878	blood:	n/a	n/a
46	POLR2A	chr1:156217208-156218302	H1-hESC	embryonic stem cell:	n/a	n/a
47	STAT5A	chr1:156217038-156218174	GM12878	blood:	n/a	chr1:156218056-156218064
48	POLR2A	chr1:156216324-156218262	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr1:156216261-156218292	K562	blood:	n/a	n/a
50	POLR2A	chr1:156217429-156218260	HepG2	liver:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:156218113-156218163	AoSMC	blood vessel:	n/a
2	chr1:156218113-156218163	NT2-D1	testis:	n/a
3	chr1:156218094-156218144	A549	lung:	n/a
4	chr1:156218113-156218163	T-47D	breast:	n/a
5	chr1:156218094-156218144	GM19239	blood:	n/a
6	chr1:156218094-156218144	BJ	skin:	n/a
7	chr1:156218113-156218163	A549	lung:	n/a
8	chr1:156218094-156218144	HCPEpiC	choroid plexus:	n/a
9	chr1:156218094-156218144	HRE	kidney:	n/a
10	chr1:156218094-156218144	SKMC	muscle:	n/a
11	chr1:156218113-156218163	HepG2	liver:	n/a
12	chr1:156218113-156218163	NB4	blood:	n/a
13	chr1:156218094-156218144	NHDF-neo	bronchial:	n/a
14	chr1:156218094-156218144	LNCaP	prostate:	n/a
15	chr1:156218113-156218163	IMR90	lung:	fetal
16	chr1:156218094-156218144	AG09309	skin:	n/a
17	chr1:156218113-156218163	Jurkat	blood:	n/a
18	chr1:156218094-156218144	GM12878	blood:	n/a
19	chr1:156218094-156218144	HNPCEpiC	eye:	n/a
20	chr1:156218094-156218144	CMK	blood:	n/a
21	chr1:156218113-156218163	HIPEpiC	eye:	n/a
22	chr1:156218113-156218163	SK-N-SH_RA	brain:	n/a
23	chr1:156218094-156218144	SK-N-MC	brain:	n/a
24	chr1:156218094-156218144	NB4	blood:	n/a
25	chr1:156218113-156218163	AG09309	skin:	n/a
26	chr1:156218113-156218163	ECC-1	luminal epithelium:	n/a
27	chr1:156218094-156218144	HUVEC	blood vessel:	n/a
28	chr1:156218113-156218163	CMK	blood:	n/a
29	chr1:156218113-156218163	K562	blood:	n/a
30	chr1:156218113-156218163	MCF-7	breast:	n/a
31	chr1:156218113-156218163	AG04449	skin:	fetal
32	chr1:156218113-156218163	NHBE	bronchial:	n/a
33	chr1:156218094-156218144	AG09319	gingival:	n/a
34	chr1:156218113-156218163	Hepatocyte	liver:	n/a
35	chr1:156218113-156218163	SK-N-SH	brain:	n/a
36	chr1:156218113-156218163	HEEpiC	esophagus:	n/a
37	chr1:156218113-156218163	PFSK-1	brain:	n/a
38	chr1:156218094-156218144	Hepatocyte	liver:	n/a
39	chr1:156218094-156218144	HEK293	kidney:	embryo
40	chr1:156218094-156218144	ovcar-3	ovarian:	n/a
41	chr1:156218094-156218144	HepG2	liver:	n/a
42	chr1:156218113-156218163	GM12878	blood:	n/a
43	chr1:156218113-156218163	HUVEC	blood vessel:	n/a
44	chr1:156218094-156218144	HRPEpiC	eye:	n/a
45	chr1:156218113-156218163	RPTEC	kidney:	n/a
46	chr1:156218113-156218163	ovcar-3	ovarian:	n/a
47	chr1:156218094-156218144	GM12892	blood:	n/a
48	chr1:156218113-156218163	HCPEpiC	choroid plexus:	n/a
49	chr1:156218094-156218144	HMEC	breast:	n/a
50	chr1:156218094-156218144	IMR90	lung:	fetal

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:156122700..156125360-chr1:156215691..156218438,2	MCF-7	breast:
2	chr1:156216698..156219216-chr1:156259674..156262599,2	K562	blood:

No data

Variant related genes	Relation type
PAQR6	TF binding region
PAQR6	CpG island
ENSG00000196189	Chromatin interaction
ENSG00000198715	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1800247	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2246476	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.92[ASN][1000 genomes]
rs2253358	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2495269	0.94[CEU][hapmap];0.95[CHB][hapmap];0.88[YRI][hapmap]
rs2540168	0.91[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2764406	0.90[CHB][hapmap];0.85[CHD][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.88[YRI][hapmap]
rs2764407	0.90[CHB][hapmap];0.88[YRI][hapmap]
rs2985711	0.82[CEU][hapmap];0.85[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	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases
2	nsv1011302	chr1:156081561-156532624	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	380 gene(s)	inside rSNPs	diseases
3	nsv872470	chr1:156210557-156223823	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2540169	FAM189B	cis	cerebellum	SCAN
rs2540169	SPRR2B	cis	cerebellum	SCAN
rs2540169	PAQR6	cis	Whole Blood	GTEx
rs2540169	SPRR2A	cis	parietal	SCAN
rs2540169	SMG5	cis	Whole Blood	GTEx
rs2540169	PAQR6	cis	lymphoblastoid	seeQTL
rs2540169	C1orf61	cis	cerebellum	SCAN
rs2540169	C1orf85	cis	Whole Blood	GTEx
rs2540169	TCHHL1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:156208200-156220000	Weak transcription	K562	blood
2	chr1:156209800-156219200	Weak transcription	Aorta	Aorta
3	chr1:156210000-156218800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:156211400-156219000	Weak transcription	Dnd41	blood
5	chr1:156211600-156251600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:156214400-156218200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr1:156214400-156233000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:156215200-156218200	Flanking Active TSS	Brain Hippocampus Middle	brain
9	chr1:156215200-156218800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr1:156215800-156218200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:156215800-156218200	Enhancers	Lung	lung
12	chr1:156215800-156218800	Enhancers	H1 Cell Line	embryonic stem cell
13	chr1:156215800-156222000	Weak transcription	Fetal Kidney	kidney
14	chr1:156216000-156218200	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr1:156216000-156218200	Enhancers	Esophagus	oesophagus
16	chr1:156216000-156218200	Enhancers	Gastric	stomach
17	chr1:156216000-156218200	Enhancers	Right Ventricle	heart
18	chr1:156216000-156218200	Enhancers	NHEK	skin
19	chr1:156216000-156218800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:156216000-156218800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:156216000-156218800	Weak transcription	Primary T cells from cord blood	blood
22	chr1:156216000-156220200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:156216000-156221200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:156216200-156218200	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr1:156216200-156218200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:156216200-156218400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:156216200-156218600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:156216200-156219800	Weak transcription	Primary B cells from cord blood	blood
29	chr1:156216200-156220000	Weak transcription	Primary B cells from peripheral blood	blood
30	chr1:156216200-156220800	Weak transcription	Psoas Muscle	Psoas
31	chr1:156216200-156221000	Weak transcription	HUVEC	blood vessel
32	chr1:156216200-156221000	Weak transcription	NHDF-Ad	bronchial
33	chr1:156216400-156218200	Enhancers	Duodenum Mucosa	Duodenum
34	chr1:156216400-156218200	Enhancers	HepG2	liver
35	chr1:156216400-156218600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr1:156216400-156218600	Enhancers	Hela-S3	cervix
37	chr1:156216400-156218800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:156216400-156218800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr1:156216400-156218800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:156216400-156218800	Weak transcription	Liver	Liver
41	chr1:156216400-156219200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:156216400-156219200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:156216400-156219400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr1:156216400-156219400	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr1:156216400-156220200	Weak transcription	GM12878-XiMat	blood
46	chr1:156216400-156221400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr1:156216400-156221400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr1:156216400-156221600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:156216400-156221800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:156216400-156224600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood

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