Variant report

Variant	rs2038753
Chromosome Location	chr1:150206698-150206699
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	POLR2A	chr1:150206581-150209771	GM12892	blood:	n/a	n/a
2	EGR1	chr1:150206273-150206851	K562	blood:	n/a	chr1:150206549-150206562 chr1:150206552-150206561 chr1:150206550-150206564 chr1:150206549-150206562 chr1:150206548-150206563 chr1:150206549-150206563 chr1:150206550-150206561 chr1:150206548-150206558 chr1:150206549-150206562 chr1:150206543-150206556 chr1:150206549-150206562 chr1:150206552-150206562 chr1:150206545-150206567
3	GTF2F1	chr1:150206459-150207418	Hela-S3	cervix:	n/a	n/a
4	PML	chr1:150206320-150209719	GM12878	blood:	n/a	chr1:150208068-150208077
5	STAT5A	chr1:150206218-150209018	GM12878	blood:	n/a	chr1:150206545-150206557 chr1:150206734-150206746
6	TBP	chr1:150206684-150207442	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:150206691-150209688	K562	blood:	n/a	n/a
8	NFATC1	chr1:150206073-150207549	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:150205972-150209097	HL-60	blood:	n/a	n/a
10	NR2F2	chr1:150205918-150206700	MCF-7	breast:	n/a	n/a
11	TEAD4	chr1:150205998-150207537	K562	blood:	n/a	n/a
12	MXI1	chr1:150206515-150209184	IMR90	lung:	n/a	n/a
13	POLR2A	chr1:150206623-150209758	GM12892	blood:	n/a	n/a
14	POLR2A	chr1:150206620-150207616	PFSK-1	brain:	n/a	n/a
15	SIN3AK20	chr1:150205702-150209385	MCF-7	breast:	n/a	n/a
16	BHLHE40	chr1:150206400-150207543	GM12878	blood:	n/a	chr1:150206545-150206561
17	CEBPB	chr1:150206210-150206738	A549	lung:	n/a	n/a
18	RCOR1	chr1:150206458-150209165	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr1:150205956-150209660	GM12891	blood:	n/a	n/a
20	POLR2A	chr1:150206617-150209688	SK-N-MC	brain:	n/a	n/a
21	MAFK	chr1:150206384-150207266	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr1:150206669-150207500	MCF10A-Er-Src	breast:	n/a	n/a
23	HDAC2	chr1:150205952-150209231	MCF-7	breast:	n/a	chr1:150206648-150206662 chr1:150208282-150208296 chr1:150206647-150206661 chr1:150206644-150206658
24	ZNF384	chr1:150206167-150207262	GM12878	blood:	n/a	n/a
25	STAT3	chr1:150206316-150207204	MCF10A-Er-Src	breast:	n/a	chr1:150207021-150207032 chr1:150206545-150206557 chr1:150206734-150206746
26	RELA	chr1:150206454-150207491	GM15510	blood:	n/a	n/a
27	TRIM28	chr1:150206574-150207375	K562	blood:	n/a	n/a
28	POLR2A	chr1:150206671-150207521	PANC-1	pancreas:	n/a	n/a
29	BCL3	chr1:150206122-150207237	A549	lung:	n/a	chr1:150207027-150207036 chr1:150206979-150206992
30	POLR2A	chr1:150206696-150209657	GM19099	blood:	n/a	n/a
31	POLR2A	chr1:150206623-150209914	PFSK-1	brain:	n/a	n/a
32	RELA	chr1:150206379-150207479	GM18505	blood:	n/a	n/a
33	ZNF384	chr1:150206337-150207281	K562	blood:	n/a	n/a
34	RELA	chr1:150205988-150209001	GM12891	blood:	n/a	n/a
35	MYC	chr1:150206316-150207339	MCF10A-Er-Src	breast:	n/a	chr1:150206549-150206559
36	POLR2A	chr1:150205839-150209223	HL-60	blood:	n/a	n/a
37	MAZ	chr1:150205735-150209200	IMR90	lung:	n/a	chr1:150208066-150208075 chr1:150206549-150206559 chr1:150207801-150207811 chr1:150207729-150207738
38	FOXM1	chr1:150206456-150207876	GM12878	blood:	n/a	n/a
39	PAX5	chr1:150206684-150207325	GM12878	blood:	n/a	n/a
40	ATF2	chr1:150206536-150207414	GM12878	blood:	n/a	n/a
41	POLR2A	chr1:150206616-150207734	Hela-S3	cervix:	n/a	n/a
42	MYC	chr1:150206290-150209144	NB4	blood:	n/a	chr1:150208066-150208075 chr1:150206549-150206559 chr1:150207801-150207811 chr1:150207729-150207738
43	FOXA2	chr1:150205983-150206881	HepG2	liver:	n/a	n/a
44	PML	chr1:150206208-150207704	K562	blood:	n/a	n/a
45	POLR2A	chr1:150206158-150209657	GM12878	blood:	n/a	n/a
46	POLR2A	chr1:150206681-150209115	GM12891	blood:	n/a	n/a
47	POLR2A	chr1:150206547-150207575	U87	brain:	n/a	n/a
48	CREB1	chr1:150206633-150207886	GM12878	blood:	n/a	n/a
49	TAF1	chr1:150206687-150209141	H1-hESC	embryonic stem cell:	n/a	n/a
50	ATF2	chr1:150206634-150207534	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:150206253..150206969-chr17:71227981..71228545,2	Hela-S3	cervix:
2	chr1:150206431..150207429-chr3:184080473..184081314,2	Hela-S3	cervix:
3	chr1:149980534..149984301-chr1:150205783..150209955,5	K562	blood:
4	chr1:150206170..150208675-chr1:150264452..150269195,6	MCF-7	breast:
5	chr1:150203436..150211066-chr1:150333611..150339492,20	K562	blood:
6	chr1:149870500..149872892-chr1:150205749..150208479,2	MCF-7	breast:
7	chr1:150205674..150207849-chr1:150521366..150523683,3	K562	blood:
8	chr1:150193027..150195228-chr1:150205376..150206988,2	MCF-7	breast:
9	chr1:150206345..150209742-chr1:150239312..150243074,6	K562	blood:
10	chr1:150205825..150209635-chr1:150259375..150267858,10	K562	blood:
11	chr1:150206250..150210524-chr1:150335148..150338813,9	MCF-7	breast:
12	chr1:150205879..150210456-chr1:150251557..150256195,8	MCF-7	breast:
13	chr1:150204090..150209498-chr1:150239337..150243073,9	K562	blood:
14	chr1:149857476..149860799-chr1:150206355..150210783,8	K562	blood:
15	chr1:150120783..150123550-chr1:150205612..150208208,2	K562	blood:
16	chr1:150206607..150208543-chr1:202994466..202996116,2	MCF-7	breast:
17	chr1:150175161..150177546-chr1:150204659..150206770,2	K562	blood:
18	chr1:149857691..149860946-chr1:150205716..150209343,6	MCF-7	breast:
19	chr1:150205006..150208304-chr1:150532619..150536152,3	MCF-7	breast:
20	chr1:150205585..150207162-chr1:150228414..150230615,2	K562	blood:
21	chr1:150198495..150205043-chr1:150206226..150211170,11	MCF-7	breast:
22	chr1:150121582..150124449-chr1:150206466..150208946,2	MCF-7	breast:
23	chr1:150205150..150208917-chr1:150946080..150950396,4	MCF-7	breast:
24	chr1:150205585..150209843-chr1:150227901..150231226,5	K562	blood:
25	chr1:150204882..150207260-chr1:150266148..150269015,2	MCF-7	breast:
26	chr1:150205053..150211036-chr1:150333116..150338498,15	K562	blood:
27	chr1:150206579..150210456-chr1:150238390..150242863,9	MCF-7	breast:
28	chr1:150182307..150185860-chr1:150205787..150209000,3	K562	blood:

Variant related genes	Relation type
RNU2-17P	TF binding region
ENSG00000143418	Chromatin interaction
ENSG00000225996	Chromatin interaction
ENSG00000163882	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000203804	Chromatin interaction
ENSG00000271845	Chromatin interaction
ENSG00000141219	Chromatin interaction
ENSG00000159208	Chromatin interaction
ENSG00000023902	Chromatin interaction
ENSG00000133193	Chromatin interaction
ENSG00000143401	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000143382	Chromatin interaction
ENSG00000117362	Chromatin interaction
ENSG00000163113	Chromatin interaction
ENSG00000187145	Chromatin interaction
ENSG00000118292	Chromatin interaction
ENSG00000143847	Chromatin interaction
ENSG00000118298	Chromatin interaction
ENSG00000266187	Chromatin interaction
ENSG00000178096	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10788872	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10888575	0.94[ASN][1000 genomes]
rs10888576	0.99[ASN][1000 genomes]
rs11205339	0.94[ASN][1000 genomes]
rs11205340	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11205343	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11205347	0.96[ASN][1000 genomes]
rs11205348	0.94[ASN][1000 genomes]
rs11811787	0.99[ASN][1000 genomes]
rs12057558	0.84[EUR][1000 genomes]
rs12131063	0.94[ASN][1000 genomes]
rs12133235	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12133238	0.94[ASN][1000 genomes]
rs12569047	0.93[ASN][1000 genomes]
rs1535873	0.94[ASN][1000 genomes]
rs1924549	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2038752	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3118124	0.94[ASN][1000 genomes]
rs3121000	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3121001	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35938158	0.83[EUR][1000 genomes]
rs4408187	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55647200	0.99[ASN][1000 genomes]
rs55956539	0.99[ASN][1000 genomes]
rs59507173	0.94[ASN][1000 genomes]
rs61161619	0.95[ASN][1000 genomes]
rs6587753	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6655935	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6660127	0.94[ASN][1000 genomes]
rs6665499	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6680040	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6682434	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6692738	0.94[ASN][1000 genomes]
rs6694215	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703332	0.92[ASN][1000 genomes]
rs7522034	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7532164	0.94[ASN][1000 genomes]
rs7548543	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551023	0.94[ASN][1000 genomes]
rs7555995	0.96[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	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150186200-150206800	Weak transcription	Spleen	Spleen
2	chr1:150186400-150206800	Weak transcription	Esophagus	oesophagus
3	chr1:150186800-150206800	Weak transcription	Pancreas	Pancrea
4	chr1:150192800-150206800	Weak transcription	Gastric	stomach
5	chr1:150200000-150206800	Weak transcription	Lung	lung
6	chr1:150201000-150206800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:150202200-150206800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:150205000-150208800	Active TSS	GM12878-XiMat	blood
9	chr1:150205800-150206800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr1:150205800-150206800	Flanking Active TSS	Brain Germinal Matrix	brain
11	chr1:150205800-150206800	Flanking Active TSS	Fetal Thymus	thymus
12	chr1:150205800-150207000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr1:150205800-150207000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:150205800-150207000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:150205800-150208800	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr1:150205800-150209000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:150205800-150209000	Active TSS	Left Ventricle	heart
18	chr1:150205800-150209400	Active TSS	Psoas Muscle	Psoas
19	chr1:150206000-150207000	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr1:150206000-150207000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr1:150206000-150207400	Active TSS	Right Atrium	heart
22	chr1:150206000-150208800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:150206000-150208800	Active TSS	Fetal Kidney	kidney
24	chr1:150206000-150209000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:150206000-150209000	Active TSS	HMEC	breast
26	chr1:150206000-150209200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:150206000-150209200	Active TSS	Brain Angular Gyrus	brain
28	chr1:150206000-150209200	Active TSS	Brain Substantia Nigra	brain
29	chr1:150206000-150209400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:150206000-150209600	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr1:150206200-150207000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr1:150206200-150207000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:150206200-150207000	Flanking Active TSS	Liver	Liver
34	chr1:150206200-150207000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr1:150206200-150208800	Active TSS	Primary T cells from cord blood	blood
36	chr1:150206200-150208800	Active TSS	Fetal Stomach	stomach
37	chr1:150206200-150209000	Active TSS	Fetal Heart	heart
38	chr1:150206200-150209200	Active TSS	Fetal Brain Male	brain
39	chr1:150206200-150209200	Active TSS	HSMM	muscle
40	chr1:150206200-150209400	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr1:150206200-150209400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr1:150206200-150209600	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr1:150206200-150209600	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr1:150206400-150206800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:150206400-150206800	Flanking Active TSS	Colonic Mucosa	Colon
46	chr1:150206400-150207000	Flanking Active TSS	Primary B cells from peripheral blood	blood
47	chr1:150206400-150207000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:150206400-150207000	Flanking Active TSS	Dnd41	blood
49	chr1:150206400-150207400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:150206400-150207600	Active TSS	Adipose Nuclei	Adipose

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