Variant report

Variant	rs971173
Chromosome Location	chr1:114447914-114447915
allele	A/C
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	CTCF	chr1:114447800-114447950	AG09309	skin:	n/a	chr1:114447874-114447892 chr1:114447876-114447889 chr1:114447880-114447889 chr1:114447875-114447891
2	TBP	chr1:114447191-114448525	H1-hESC	embryonic stem cell:	n/a	n/a
3	ELF1	chr1:114447141-114448206	GM12878	blood:	n/a	n/a
4	REST	chr1:114447780-114447992	PANC-1	pancreas:	n/a	chr1:114447859-114447872
5	MAX	chr1:114446705-114448409	K562	blood:	n/a	chr1:114447122-114447131
6	MYC	chr1:114447491-114448011	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZKSCAN1	chr1:114446919-114448391	Hela-S3	cervix:	n/a	n/a
8	E2F6	chr1:114446833-114448388	K562	blood:	n/a	n/a
9	KAP1	chr1:114447068-114448319	U2OS	brain:	n/a	n/a
10	TCF12	chr1:114447628-114448065	H1-hESC	embryonic stem cell:	n/a	n/a
11	RAD21	chr1:114447600-114448028	A549	lung:	n/a	chr1:114447872-114447891 chr1:114447996-114448008
12	MYC	chr1:114447138-114448107	MCF-7	breast:	n/a	n/a
13	MAFK	chr1:114447205-114448048	HepG2	liver:	n/a	n/a
14	MYC	chr1:114446758-114448458	Hela-S3	cervix:	n/a	chr1:114447122-114447131
15	MAFK	chr1:114447005-114448536	K562	blood:	n/a	n/a
16	CHD2	chr1:114446998-114448470	Hela-S3	cervix:	n/a	n/a
17	RCOR1	chr1:114446593-114448470	Hela-S3	cervix:	n/a	n/a
18	CEBPB	chr1:114446772-114448431	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr1:114447758-114448018	Gliobla	brain:	n/a	chr1:114447874-114447892 chr1:114447876-114447889 chr1:114447880-114447889 chr1:114447875-114447891
20	THAP1	chr1:114447768-114448023	K562	blood:	n/a	n/a
21	CTCF	chr1:114447800-114447950	HBMEC	blood vessel:	n/a	chr1:114447874-114447892 chr1:114447876-114447889 chr1:114447880-114447889 chr1:114447875-114447891
22	RCOR1	chr1:114447087-114448043	HepG2	liver:	n/a	n/a
23	SIN3AK20	chr1:114447701-114448323	K562	blood:	n/a	n/a
24	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
25	ETS1	chr1:114447218-114448175	A549	lung:	n/a	chr1:114447728-114447744
26	CTCF	chr1:114447802-114447971	SK-N-SH_RA	brain:	n/a	chr1:114447874-114447892 chr1:114447876-114447889 chr1:114447880-114447889 chr1:114447875-114447891
27	CTCF	chr1:114447780-114447930	HL-60	blood:	n/a	chr1:114447874-114447892 chr1:114447876-114447889 chr1:114447880-114447889 chr1:114447875-114447891
28	BRCA1	chr1:114446971-114448213	Hela-S3	cervix:	n/a	n/a
29	RAD21	chr1:114447691-114448074	HepG2	liver:	n/a	chr1:114448017-114448030 chr1:114447872-114447891 chr1:114447996-114448008
30	RAD21	chr1:114447456-114448090	K562	blood:	n/a	chr1:114448017-114448030 chr1:114447872-114447891 chr1:114447996-114448008
31	CTCF	chr1:114447900-114448050	A549	lung:	n/a	chr1:114448016-114448029
32	ATF2	chr1:114447554-114448063	H1-hESC	embryonic stem cell:	n/a	n/a
33	YY1	chr1:114447485-114448148	SK-N-SH_RA	brain:	n/a	chr1:114447969-114447980
34	YY1	chr1:114447394-114448162	ECC-1	luminal epithelium:	n/a	chr1:114447969-114447980
35	GTF2F1	chr1:114447853-114447980	H1-hESC	embryonic stem cell:	n/a	n/a
36	GABPA	chr1:114447255-114448272	K562	blood:	n/a	n/a
37	MYC	chr1:114447353-114448349	MCF-7	breast:	n/a	n/a
38	EP300	chr1:114447561-114448094	HepG2	liver:	n/a	n/a
39	POLR2A	chr1:114447744-114448076	H1-hESC	embryonic stem cell:	n/a	n/a
40	CCNT2	chr1:114446648-114448457	K562	blood:	n/a	n/a
41	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
42	REST	chr1:114447608-114448069	SK-N-SH	brain:	n/a	chr1:114447859-114447872
43	PML	chr1:114446940-114448489	K562	blood:	n/a	n/a
44	POLR2A	chr1:114447771-114448267	GM12892	blood:	n/a	n/a
45	POLR2A	chr1:114447859-114448117	HepG2	liver:	n/a	n/a
46	POLR2A	chr1:114446629-114448290	IMR90	lung:	n/a	n/a
47	POLR2A	chr1:114447031-114448314	HepG2	liver:	n/a	n/a
48	SRF	chr1:114447734-114448027	GM12878	blood:	n/a	n/a
49	CTCF	chr1:114447840-114447990	GM12801	blood:	n/a	chr1:114447874-114447892 chr1:114447876-114447889 chr1:114447880-114447889 chr1:114447875-114447891
50	CTCF	chr1:114447710-114448032	H1-hESC	embryonic stem cell:	n/a	chr1:114447874-114447892 chr1:114447746-114447756 chr1:114447876-114447889 chr1:114447880-114447889 chr1:114447875-114447891 chr1:114448016-114448029

No.	Distal block	Cell Line	Cell type
1	chr1:114447837..114448427-chr1:151583823..151584662,2	Hela-S3	cervix:
2	chr1:114445859..114448805-chr17:42295421..42298283,3	MCF-7	breast:
3	chr1:114446008..114448199-chr1:114495493..114497584,2	MCF-7	breast:
4	chr1:113257309..113258998-chr1:114446539..114449479,2	K562	blood:
5	chr1:114352137..114357235-chr1:114445065..114452395,18	MCF-7	breast:
6	chr1:114301575..114302482-chr1:114447707..114448378,2	MCF-7	breast:
7	chr1:114446374..114449379-chr1:115298741..115300876,3	MCF-7	breast:
8	chr1:114299428..114302166-chr1:114446012..114448303,2	K562	blood:
9	chr1:114447415..114448376-chr1:114471694..114473083,5	MCF-7	breast:
10	chr1:114444168..114452207-chr1:114466193..114476714,61	K562	blood:
11	chr1:114353683..114357770-chr1:114446246..114449576,8	K562	blood:
12	chr1:114445068..114448942-chr1:115050232..115055017,4	MCF-7	breast:
13	chr1:114447396..114448619-chr1:114471602..114472886,11	MCF-7	breast:
14	chr1:114446165..114448738-chr1:115053730..115055909,2	MCF-7	breast:
15	chr1:114446144..114448333-chr19:16187175..16189942,2	MCF-7	breast:
16	chr1:114447360..114448137-chr3:50126334..50127160,2	NB4	blood:
17	chr1:114447369..114448385-chr1:114471257..114473158,18	MCF-7	breast:
18	chr1:114447581..114448246-chr1:114471806..114472560,3	HCT-116	colon:
19	chr1:114300712..114302958-chr1:114446093..114449659,3	MCF-7	breast:
20	chr1:114352306..114358140-chr1:114445806..114450844,18	MCF-7	breast:
21	chr1:114300422..114303875-chr1:114445198..114448512,7	MCF-7	breast:
22	chr1:114353620..114357151-chr1:114445438..114449458,6	K562	blood:
23	chr1:114300393..114302237-chr1:114446494..114449478,3	K562	blood:
24	chr1:114447790..114448383-chr1:114471947..114472675,2	NB4	blood:
25	chr1:114447832..114448433-chr1:114472824..114473410,2	Hela-S3	cervix:
26	chr1:114363592..114366555-chr1:114447214..114449427,2	MCF-7	breast:
27	chr1:114447452..114448400-chr1:114471566..114472757,4	Hela-S3	cervix:
28	chr1:114447178..114448996-chr1:114471115..114472973,22	MCF-7	breast:

Variant related genes	Relation type
DCLRE1B	TF binding region
AP4B1	TF binding region
ENSG00000108312	Chromatin interaction
ENSG00000116793	Chromatin interaction
ENSG00000231128	Chromatin interaction
ENSG00000167460	Chromatin interaction
ENSG00000261595	Chromatin interaction
ENSG00000081019	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000143376	Chromatin interaction
ENSG00000235527	Chromatin interaction
ENSG00000009307	Chromatin interaction
ENSG00000197323	Chromatin interaction
ENSG00000003756	Chromatin interaction
ENSG00000155367	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11102678	0.90[JPT][hapmap]
rs11102695	0.86[CEU][hapmap]
rs1217375	0.90[JPT][hapmap];0.82[MEX][hapmap]
rs1217382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs1217393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1217397	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]
rs1217400	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1217401	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1217403	0.90[JPT][hapmap]
rs1217408	0.90[JPT][hapmap]
rs1217414	0.86[CEU][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap]
rs1217423	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1230681	0.90[JPT][hapmap]
rs1310183	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1746860	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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];0.82[MEX][hapmap]
rs3789597	0.90[JPT][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs971173	BCL2L15	cis	cerebellum	SCAN
rs971173	AP4B1	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	chr1:114446400-114448600	Active TSS	Aorta	Aorta
6	chr1:114446400-114448600	Active TSS	Psoas Muscle	Psoas
7	chr1:114446400-114448600	Active TSS	Right Atrium	heart
8	chr1:114446400-114449200	Active TSS	A549	lung
9	chr1:114446400-114449600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:114446600-114448200	Active TSS	Fetal Muscle Trunk	muscle
11	chr1:114446600-114448200	Active TSS	Left Ventricle	heart
12	chr1:114446600-114448200	Active TSS	Lung	lung
13	chr1:114446600-114448600	Active TSS	H9 Cell Line	embryonic stem cell
14	chr1:114446600-114448600	Active TSS	Esophagus	oesophagus
15	chr1:114446600-114448600	Active TSS	Pancreas	Pancrea
16	chr1:114446600-114448800	Active TSS	NHDF-Ad	bronchial
17	chr1:114446600-114449400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:114446800-114448200	Active TSS	Right Ventricle	heart
19	chr1:114446800-114448400	Active TSS	Spleen	Spleen
20	chr1:114446800-114448600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:114446800-114448600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:114446800-114448600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:114446800-114448600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:114446800-114448600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:114446800-114448600	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr1:114446800-114448600	Active TSS	Gastric	stomach
27	chr1:114446800-114448600	Active TSS	Ovary	ovary
28	chr1:114446800-114448600	Active TSS	Small Intestine	intestine
29	chr1:114446800-114448600	Bivalent/Poised TSS	HepG2	liver
30	chr1:114446800-114448800	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr1:114446800-114448800	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr1:114446800-114448800	Active TSS	Fetal Stomach	stomach
33	chr1:114446800-114449000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:114446800-114449000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:114446800-114449000	Active TSS	NHLF	lung
36	chr1:114447000-114448000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:114447000-114448200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:114447000-114448200	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr1:114447000-114448200	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr1:114447000-114448200	Active TSS	Duodenum Mucosa	Duodenum
41	chr1:114447000-114448200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr1:114447000-114448200	Active TSS	Fetal Muscle Leg	muscle
43	chr1:114447000-114448200	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr1:114447000-114448200	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr1:114447000-114448200	Active TSS	Thymus	Thymus
46	chr1:114447000-114448200	Active TSS	Monocytes-CD14+_RO01746	blood
47	chr1:114447000-114448400	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr1:114447000-114448400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:114447000-114448400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr1:114447000-114448400	Active TSS	Brain Anterior Caudate	brain

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