Variant report

Variant	rs1217397
Chromosome Location	chr1:114447565-114447566
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:504)
CpG islands
(count:61)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:504 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr1:114447191-114448525	H1-hESC	embryonic stem cell:	n/a	n/a
2	ELF1	chr1:114447141-114448206	GM12878	blood:	n/a	n/a
3	MAX	chr1:114446705-114448409	K562	blood:	n/a	chr1:114447122-114447131
4	MYC	chr1:114447491-114448011	H1-hESC	embryonic stem cell:	n/a	n/a
5	ZKSCAN1	chr1:114446919-114448391	Hela-S3	cervix:	n/a	n/a
6	TAF1	chr1:114447123-114447616	A549	lung:	n/a	n/a
7	E2F6	chr1:114446833-114448388	K562	blood:	n/a	n/a
8	KAP1	chr1:114447068-114448319	U2OS	brain:	n/a	n/a
9	MYC	chr1:114447138-114448107	MCF-7	breast:	n/a	n/a
10	MAFK	chr1:114447205-114448048	HepG2	liver:	n/a	n/a
11	MYC	chr1:114446758-114448458	Hela-S3	cervix:	n/a	chr1:114447122-114447131
12	MAFK	chr1:114447005-114448536	K562	blood:	n/a	n/a
13	CHD2	chr1:114446998-114448470	Hela-S3	cervix:	n/a	n/a
14	RCOR1	chr1:114446593-114448470	Hela-S3	cervix:	n/a	n/a
15	CEBPB	chr1:114446772-114448431	Hela-S3	cervix:	n/a	n/a
16	RCOR1	chr1:114447087-114448043	HepG2	liver:	n/a	n/a
17	SP1	chr1:114447153-114448255	A549	lung:	n/a	chr1:114447658-114447669 chr1:114447741-114447753 chr1:114447741-114447753 chr1:114447583-114447594 chr1:114447835-114447849 chr1:114447742-114447756 chr1:114447743-114447752 chr1:114447742-114447751
18	ETS1	chr1:114447218-114448175	A549	lung:	n/a	chr1:114447728-114447744
19	BRCA1	chr1:114446971-114448213	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr1:114447208-114447735	HepG2	liver:	n/a	n/a
21	RAD21	chr1:114447456-114448090	K562	blood:	n/a	chr1:114448017-114448030 chr1:114447872-114447891 chr1:114447996-114448008
22	ATF2	chr1:114447554-114448063	H1-hESC	embryonic stem cell:	n/a	n/a
23	YY1	chr1:114447485-114448148	SK-N-SH_RA	brain:	n/a	chr1:114447969-114447980
24	YY1	chr1:114447394-114448162	ECC-1	luminal epithelium:	n/a	chr1:114447969-114447980
25	GABPA	chr1:114447255-114448272	K562	blood:	n/a	n/a
26	MYC	chr1:114447353-114448349	MCF-7	breast:	n/a	n/a
27	EP300	chr1:114447561-114448094	HepG2	liver:	n/a	n/a
28	CCNT2	chr1:114446648-114448457	K562	blood:	n/a	n/a
29	SP1	chr1:114447256-114448142	GM12878	blood:	n/a	chr1:114447658-114447669 chr1:114447741-114447753 chr1:114447741-114447753 chr1:114447583-114447594 chr1:114447835-114447849 chr1:114447742-114447756 chr1:114447743-114447752 chr1:114447742-114447751
30	PML	chr1:114446940-114448489	K562	blood:	n/a	n/a
31	POLR2A	chr1:114446629-114448290	IMR90	lung:	n/a	n/a
32	HEY1	chr1:114447069-114447670	K562	blood:	n/a	n/a
33	POLR2A	chr1:114447031-114448314	HepG2	liver:	n/a	n/a
34	PAX5	chr1:114447158-114448179	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:114446190-114448381	GM18505	blood:	n/a	n/a
36	POLR2A	chr1:114447054-114447598	GM12878	blood:	n/a	n/a
37	RAD21	chr1:114447041-114448485	HCT-116	colon:	n/a	chr1:114448017-114448030 chr1:114447872-114447891 chr1:114447996-114448008
38	EP300	chr1:114446732-114448152	GM12878	blood:	n/a	n/a
39	TCF12	chr1:114447219-114448578	ECC-1	luminal epithelium:	n/a	n/a
40	MAX	chr1:114445917-114448671	MCF-7	breast:	n/a	chr1:114448611-114448620 chr1:114447122-114447131
41	POLR2A	chr1:114446410-114448235	GM12878	blood:	n/a	n/a
42	POLR2A	chr1:114446876-114448536	GM18526	blood:	n/a	n/a
43	EGR1	chr1:114447411-114448122	K562	blood:	n/a	n/a
44	POLR2A	chr1:114447267-114448108	HepG2	liver:	n/a	n/a
45	POLR2A	chr1:114446984-114448445	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr1:114446816-114448383	ProgFib	skin:	n/a	n/a
47	POLR2A	chr1:114447273-114447673	HepG2	liver:	n/a	n/a
48	CREB1	chr1:114447091-114448149	GM12878	blood:	n/a	n/a
49	MAX	chr1:114446759-114448244	HUVEC	blood vessel:	n/a	chr1:114447122-114447131
50	MXI1	chr1:114446060-114448767	SK-N-SH	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:114447516-114447566	HepG2	liver:	n/a
2	chr1:114447516-114447566	NHDF-neo	bronchial:	n/a
3	chr1:114447516-114447566	BJ	skin:	n/a
4	chr1:114447516-114447566	GM06990	blood:	n/a
5	chr1:114447516-114447566	HEEpiC	esophagus:	n/a
6	chr1:114447516-114447566	ECC-1	luminal epithelium:	n/a
7	chr1:114447516-114447566	GM12891	blood:	n/a
8	chr1:114447516-114447566	LNCaP	prostate:	n/a
9	chr1:114447516-114447566	ProgFib	skin:	n/a
10	chr1:114447516-114447566	NT2-D1	testis:	n/a
11	chr1:114447516-114447566	AG09309	skin:	n/a
12	chr1:114447516-114447566	HMEC	breast:	n/a
13	chr1:114447516-114447566	HAEpiC	amniotic membrane:	n/a
14	chr1:114447516-114447566	AG04450	lung:	fetal
15	chr1:114447516-114447566	Caco-2	colon:	n/a
16	chr1:114447516-114447566	AG04449	skin:	fetal
17	chr1:114447516-114447566	HRPEpiC	eye:	n/a
18	chr1:114447516-114447566	GM19239	blood:	n/a
19	chr1:114447516-114447566	PANC-1	pancreas:	n/a
20	chr1:114447516-114447566	NHBE	bronchial:	n/a
21	chr1:114447516-114447566	SK-N-MC	brain:	n/a
22	chr1:114447516-114447566	BE2_C	brain:	n/a
23	chr1:114447516-114447566	SK-N-SH	brain:	n/a
24	chr1:114447516-114447566	NH-A	brain:	n/a
25	chr1:114447516-114447566	SKMC	muscle:	n/a
26	chr1:114447516-114447566	MCF10A-Er-Src	breast:	n/a
27	chr1:114447516-114447566	Jurkat	blood:	n/a
28	chr1:114447516-114447566	GM12878	blood:	n/a
29	chr1:114447516-114447566	HPAEpiC	pulmonary alveolar:	n/a
30	chr1:114447516-114447566	SAEC	small airway:	n/a
31	chr1:114447516-114447566	IMR90	lung:	fetal
32	chr1:114447516-114447566	PrEC	prostate:	n/a
33	chr1:114447516-114447566	ovcar-3	ovarian:	n/a
34	chr1:114447516-114447566	HCF	heart:	n/a
35	chr1:114447516-114447566	HNPCEpiC	eye:	n/a
36	chr1:114447516-114447566	HRE	kidney:	n/a
37	chr1:114447516-114447566	HUVEC	blood vessel:	n/a
38	chr1:114447516-114447566	A549	lung:	n/a
39	chr1:114447516-114447566	H1-hESC	embryonic stem cell:	embryo
40	chr1:114447516-114447566	HIPEpiC	eye:	n/a
41	chr1:114447516-114447566	PFSK-1	brain:	n/a
42	chr1:114447516-114447566	RPTEC	kidney:	n/a
43	chr1:114447516-114447566	SK-N-SH_RA	brain:	n/a
44	chr1:114447516-114447566	U87	brain:	n/a
45	chr1:114447516-114447566	HEK293	kidney:	embryo
46	chr1:114447516-114447566	T-47D	breast:	n/a
47	chr1:114447516-114447566	NB4	blood:	n/a
48	chr1:114447516-114447566	HCM	heart:	n/a
49	chr1:114447516-114447566	Hela-S3	cervix:	n/a
50	chr1:114447516-114447566	HCT-116	colon:	n/a

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114445859..114448805-chr17:42295421..42298283,3	MCF-7	breast:
2	chr1:114446008..114448199-chr1:114495493..114497584,2	MCF-7	breast:
3	chr1:113257309..113258998-chr1:114446539..114449479,2	K562	blood:
4	chr1:114352137..114357235-chr1:114445065..114452395,18	MCF-7	breast:
5	chr1:114446374..114449379-chr1:115298741..115300876,3	MCF-7	breast:
6	chr1:114299428..114302166-chr1:114446012..114448303,2	K562	blood:
7	chr1:114447415..114448376-chr1:114471694..114473083,5	MCF-7	breast:
8	chr1:114444168..114452207-chr1:114466193..114476714,61	K562	blood:
9	chr1:114353683..114357770-chr1:114446246..114449576,8	K562	blood:
10	chr1:114445068..114448942-chr1:115050232..115055017,4	MCF-7	breast:
11	chr1:114447396..114448619-chr1:114471602..114472886,11	MCF-7	breast:
12	chr1:114446165..114448738-chr1:115053730..115055909,2	MCF-7	breast:
13	chr1:114446144..114448333-chr19:16187175..16189942,2	MCF-7	breast:
14	chr1:114447360..114448137-chr3:50126334..50127160,2	NB4	blood:
15	chr1:114447369..114448385-chr1:114471257..114473158,18	MCF-7	breast:
16	chr1:114300712..114302958-chr1:114446093..114449659,3	MCF-7	breast:
17	chr1:114352306..114358140-chr1:114445806..114450844,18	MCF-7	breast:
18	chr1:114300422..114303875-chr1:114445198..114448512,7	MCF-7	breast:
19	chr1:114353620..114357151-chr1:114445438..114449458,6	K562	blood:
20	chr1:114300393..114302237-chr1:114446494..114449478,3	K562	blood:
21	chr1:114363592..114366555-chr1:114447214..114449427,2	MCF-7	breast:
22	chr1:114447452..114448400-chr1:114471566..114472757,4	Hela-S3	cervix:
23	chr1:114447178..114448996-chr1:114471115..114472973,22	MCF-7	breast:

No data

Variant related genes	Relation type
DCLRE1B	TF binding region
AP4B1	TF binding region
DCLRE1B	CpG island
AP4B1	CpG island
ENSG00000003756	Chromatin interaction
ENSG00000155367	Chromatin interaction
ENSG00000116793	Chromatin interaction
ENSG00000235527	Chromatin interaction
ENSG00000009307	Chromatin interaction
ENSG00000197323	Chromatin interaction
ENSG00000108312	Chromatin interaction
ENSG00000167460	Chromatin interaction
ENSG00000081019	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000231128	Chromatin interaction
ENSG00000261595	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11102678	0.90[JPT][hapmap]
rs11102695	0.91[CEU][hapmap]
rs1217375	0.90[JPT][hapmap]
rs1217382	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs1217393	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217400	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217401	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217403	0.90[JPT][hapmap]
rs1217408	0.90[JPT][hapmap]
rs1217414	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs1217423	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1230681	0.90[JPT][hapmap]
rs1310183	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1746860	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1935836	0.90[JPT][hapmap]
rs1970559	0.90[JPT][hapmap]
rs2040041	0.90[JPT][hapmap]
rs2185827	0.90[JPT][hapmap]
rs2476599	0.90[JPT][hapmap]
rs2476602	0.90[JPT][hapmap]
rs3789597	0.90[JPT][hapmap]
rs971173	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1217397	PTPN22	cis	parietal	SCAN
rs1217397	AP4B1	cis	cerebellum	SCAN
rs1217397	BCL2L15	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114445600-114449800	Active TSS	GM12878-XiMat	blood
2	chr1:114446200-114448800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:114446200-114449000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:114446200-114449600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:114446400-114447600	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr1:114446400-114448600	Active TSS	Aorta	Aorta
7	chr1:114446400-114448600	Active TSS	Psoas Muscle	Psoas
8	chr1:114446400-114448600	Active TSS	Right Atrium	heart
9	chr1:114446400-114449200	Active TSS	A549	lung
10	chr1:114446400-114449600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:114446600-114448200	Active TSS	Fetal Muscle Trunk	muscle
12	chr1:114446600-114448200	Active TSS	Left Ventricle	heart
13	chr1:114446600-114448200	Active TSS	Lung	lung
14	chr1:114446600-114448600	Active TSS	H9 Cell Line	embryonic stem cell
15	chr1:114446600-114448600	Active TSS	Esophagus	oesophagus
16	chr1:114446600-114448600	Active TSS	Pancreas	Pancrea
17	chr1:114446600-114448800	Active TSS	NHDF-Ad	bronchial
18	chr1:114446600-114449400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:114446800-114448200	Active TSS	Right Ventricle	heart
20	chr1:114446800-114448400	Active TSS	Spleen	Spleen
21	chr1:114446800-114448600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:114446800-114448600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:114446800-114448600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:114446800-114448600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:114446800-114448600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:114446800-114448600	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr1:114446800-114448600	Active TSS	Gastric	stomach
28	chr1:114446800-114448600	Active TSS	Ovary	ovary
29	chr1:114446800-114448600	Active TSS	Small Intestine	intestine
30	chr1:114446800-114448600	Bivalent/Poised TSS	HepG2	liver
31	chr1:114446800-114448800	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr1:114446800-114448800	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr1:114446800-114448800	Active TSS	Fetal Stomach	stomach
34	chr1:114446800-114449000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:114446800-114449000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:114446800-114449000	Active TSS	NHLF	lung
37	chr1:114447000-114448000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:114447000-114448200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:114447000-114448200	Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr1:114447000-114448200	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr1:114447000-114448200	Active TSS	Duodenum Mucosa	Duodenum
42	chr1:114447000-114448200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr1:114447000-114448200	Active TSS	Fetal Muscle Leg	muscle
44	chr1:114447000-114448200	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr1:114447000-114448200	Active TSS	Sigmoid Colon	Sigmoid Colon
46	chr1:114447000-114448200	Active TSS	Thymus	Thymus
47	chr1:114447000-114448200	Active TSS	Monocytes-CD14+_RO01746	blood
48	chr1:114447000-114448400	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr1:114447000-114448400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:114447000-114448400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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