Variant report

Variant	rs385513
Chromosome Location	chr2:9983716-9983717
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	PBX3	chr2:9983124-9984027	SK-N-SH	brain:	n/a	n/a
2	PML	chr2:9983063-9984273	K562	blood:	n/a	n/a
3	ZBTB7A	chr2:9983178-9984151	K562	blood:	n/a	chr2:9983258-9983265
4	FOXA1	chr2:9983141-9984013	HepG2	liver:	n/a	n/a
5	KAP1	chr2:9982721-9984204	HEK293	kidney:	n/a	n/a
6	POLR2A	chr2:9983035-9984253	K562	blood:	n/a	n/a
7	GABPA	chr2:9982890-9984044	A549	lung:	n/a	chr2:9983539-9983553 chr2:9983542-9983553 chr2:9983542-9983551 chr2:9983542-9983556
8	TEAD4	chr2:9983151-9983846	HepG2	liver:	n/a	n/a
9	YY1	chr2:9983245-9983992	HCT-116	colon:	n/a	n/a
10	ELF1	chr2:9983146-9984177	GM12878	blood:	n/a	chr2:9983606-9983615
11	CCNT2	chr2:9983164-9984002	K562	blood:	n/a	n/a
12	RAD21	chr2:9983483-9984184	HepG2	liver:	n/a	n/a
13	SP1	chr2:9983125-9984451	A549	lung:	n/a	chr2:9983430-9983451 chr2:9984040-9984054
14	CTCF	chr2:9983620-9983770	BE2_C	brain:	n/a	n/a
15	POLR2A	chr2:9983182-9983993	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr2:9983069-9984132	HCT-116	colon:	n/a	n/a
17	ETS1	chr2:9983106-9984148	K562	blood:	n/a	chr2:9983576-9983589 chr2:9983582-9983595
18	STAT1	chr2:9982982-9984204	Hela-S3	cervix:	n/a	chr2:9983604-9983613 chr2:9984040-9984052 chr2:9983603-9983614 chr2:9983599-9983619 chr2:9983599-9983619 chr2:9983605-9983613 chr2:9983909-9983921 chr2:9983597-9983609 chr2:9983605-9983614 chr2:9984046-9984058
19	ZBTB33	chr2:9983178-9983869	A549	lung:	n/a	n/a
20	CEBPD	chr2:9983558-9983966	HepG2	liver:	n/a	n/a
21	NRF1	chr2:9983355-9984054	K562	blood:	n/a	chr2:9983539-9983553 chr2:9983542-9983553 chr2:9983541-9983552 chr2:9983542-9983551 chr2:9983542-9983556
22	CTCF	chr2:9983580-9983730	HMF	breast:	n/a	n/a
23	CTCF	chr2:9983640-9983790	GM12870	blood:	n/a	n/a
24	CBX3	chr2:9982631-9984462	K562	blood:	n/a	n/a
25	POLR2A	chr2:9983108-9984109	K562	blood:	n/a	n/a
26	MYC	chr2:9983619-9983718	MCF-7	breast:	n/a	n/a
27	MYC	chr2:9983342-9984029	MCF-7	breast:	n/a	n/a
28	YY1	chr2:9983323-9984145	GM12892	blood:	n/a	n/a
29	CTCF	chr2:9983527-9983781	Spleen_OC	spleen:	n/a	n/a
30	NFIC	chr2:9983303-9983805	HepG2	liver:	n/a	n/a
31	POLR2A	chr2:9982941-9984260	PANC-1	pancreas:	n/a	n/a
32	CHD2	chr2:9983280-9984492	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr2:9983640-9983790	HFF-Myc	foreskin:	n/a	n/a
34	CTCF	chr2:9983680-9983830	HPF	lung:	n/a	n/a
35	MYC	chr2:9983224-9984056	K562	blood:	n/a	chr2:9984044-9984054
36	POLR2A	chr2:9983160-9984376	U87	brain:	n/a	n/a
37	STAT1	chr2:9983166-9984000	K562	blood:	n/a	chr2:9983604-9983613 chr2:9983603-9983614 chr2:9983599-9983619 chr2:9983599-9983619 chr2:9983605-9983613 chr2:9983909-9983921 chr2:9983597-9983609 chr2:9983605-9983614
38	TEAD4	chr2:9983190-9984204	ECC-1	luminal epithelium:	n/a	n/a
39	HEY1	chr2:9983179-9984018	HepG2	liver:	n/a	chr2:9983540-9983555
40	ZC3H11A	chr2:9983205-9983897	K562	blood:	n/a	n/a
41	GATA3	chr2:9983478-9983995	T-47D	breast:	n/a	n/a
42	CTCF	chr2:9983640-9983790	GM12872	blood:	n/a	n/a
43	MAX	chr2:9982904-9984270	A549	lung:	n/a	chr2:9984044-9984054
44	HDAC2	chr2:9983149-9983877	H1-hESC	embryonic stem cell:	n/a	chr2:9983317-9983326 chr2:9983522-9983531
45	MYC	chr2:9983366-9984282	H1-hESC	embryonic stem cell:	n/a	chr2:9984044-9984054
46	TCF7L2	chr2:9983121-9984573	Hela-S3	cervix:	n/a	n/a
47	ELK4	chr2:9983335-9983819	Hela-S3	cervix:	n/a	chr2:9983606-9983617 chr2:9983575-9983586
48	POLR2A	chr2:9983131-9984050	HUVEC	blood vessel:	n/a	n/a
49	HDAC2	chr2:9983111-9984062	HepG2	liver:	n/a	chr2:9983317-9983326 chr2:9983522-9983531
50	PAX5	chr2:9983456-9983920	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:9983066..9987186-chr2:10091615..10095343,4	MCF-7	breast:
2	chr1:225117101..225117940-chr2:9982915..9983806,2	Hela-S3	cervix:
3	chr12:92539579..92540096-chr2:9983233..9984120,2	NB4	blood:
4	chr19:36605408..36606315-chr2:9983471..9984383,2	Hela-S3	cervix:
5	chr2:9981740..9985209-chr2:10182518..10185707,4	K562	blood:
6	chr2:9981933..9984802-chr2:10182812..10185710,3	K562	blood:
7	chr19:11199999..11200904-chr2:9983330..9983881,2	Hela-S3	cervix:
8	chr2:9983297..9984997-chr2:10260468..10262228,2	K562	blood:
9	chr2:9982271..9986804-chr2:10090021..10093067,7	K562	blood:
10	chr2:9982517..9985169-chr2:10586715..10588876,2	K562	blood:
11	chr2:9983691..9985832-chr2:10083772..10085914,3	MCF-7	breast:
12	chr2:9982957..9983900-chr3:149530307..149531181,2	Hela-S3	cervix:
13	chr2:9983262..9985223-chr2:10260728..10263822,3	K562	blood:
14	chr2:9982092..9985559-chr2:10088577..10093200,6	MCF-7	breast:
15	chr2:9982271..9985181-chr2:10090033..10093358,4	K562	blood:
16	chr2:9981748..9983787-chr2:10179341..10181254,2	K562	blood:

Variant related genes	Relation type
TAF1B	TF binding region
ENSG00000130164	Chromatin interaction
ENSG00000172059	Chromatin interaction
ENSG00000133639	Chromatin interaction
ENSG00000105254	Chromatin interaction
ENSG00000115758	Chromatin interaction
ENSG00000082996	Chromatin interaction
ENSG00000105258	Chromatin interaction
ENSG00000260077	Chromatin interaction
ENSG00000245904	Chromatin interaction
ENSG00000171848	Chromatin interaction
ENSG00000257135	Chromatin interaction
ENSG00000272524	Chromatin interaction
ENSG00000185842	Chromatin interaction
ENSG00000134317	Chromatin interaction
ENSG00000206633	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12612554	0.83[AFR][1000 genomes]
rs1652684	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs287985	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs287998	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs288000	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs288001	0.83[AFR][1000 genomes]
rs366852	0.80[AFR][1000 genomes]
rs379396	0.83[AFR][1000 genomes]
rs386006	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs396190	0.83[AFR][1000 genomes]
rs396416	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs400098	0.80[AFR][1000 genomes]
rs403303	0.86[AFR][1000 genomes]
rs406546	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs417748	0.83[AFR][1000 genomes]
rs446907	0.86[AFR][1000 genomes]
rs6744203	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013969	chr2:9888703-10023951	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv873628	chr2:9949464-9985670	Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
5	nsv873629	chr2:9949464-10016627	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
6	nsv873630	chr2:9953949-10030024	Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
7	nsv873631	chr2:9975557-10059770	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
8	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9982600-9984200	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr2:9982800-9984000	Active TSS	Liver	Liver
3	chr2:9982800-9984200	Active TSS	Brain Cingulate Gyrus	brain
4	chr2:9982800-9984200	Active TSS	Brain Hippocampus Middle	brain
5	chr2:9982800-9984200	Active TSS	Stomach Smooth Muscle	stomach
6	chr2:9982800-9984400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:9982800-9984400	Active TSS	Brain Anterior Caudate	brain
8	chr2:9982800-9984400	Active TSS	Fetal Brain Female	brain
9	chr2:9982800-9984600	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr2:9982800-9984600	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr2:9982800-9984600	Active TSS	K562	blood
12	chr2:9982800-9984600	Active TSS	NH-A	brain
13	chr2:9982800-9984800	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr2:9982800-9984800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:9982800-9984800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:9982800-9985200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:9982800-9985200	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr2:9983000-9984000	Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr2:9983000-9984200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr2:9983000-9984200	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr2:9983000-9984200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:9983000-9984200	Active TSS	Primary T cells from cord blood	blood
23	chr2:9983000-9984200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:9983000-9984200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:9983000-9984200	Active TSS	Colonic Mucosa	Colon
26	chr2:9983000-9984200	Active TSS	Fetal Lung	lung
27	chr2:9983000-9984200	Active TSS	Thymus	Thymus
28	chr2:9983000-9984200	Active TSS	HSMMtube	muscle
29	chr2:9983000-9984400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:9983000-9984400	Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr2:9983000-9984400	Active TSS	Aorta	Aorta
32	chr2:9983000-9984400	Active TSS	Brain Angular Gyrus	brain
33	chr2:9983000-9984400	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr2:9983000-9984400	Active TSS	Brain Substantia Nigra	brain
35	chr2:9983000-9984400	Active TSS	Colon Smooth Muscle	Colon
36	chr2:9983000-9984400	Active TSS	Duodenum Mucosa	Duodenum
37	chr2:9983000-9984400	Active TSS	Fetal Intestine Large	intestine
38	chr2:9983000-9984400	Active TSS	Fetal Intestine Small	intestine
39	chr2:9983000-9984400	Active TSS	Placenta Amnion	Placenta Amnion
40	chr2:9983000-9984400	Active TSS	Right Ventricle	heart
41	chr2:9983000-9984400	Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr2:9983000-9984600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr2:9983000-9984600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:9983000-9984600	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr2:9983000-9984600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr2:9983000-9984600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr2:9983000-9984600	Active TSS	Esophagus	oesophagus
48	chr2:9983000-9984600	Active TSS	Fetal Kidney	kidney
49	chr2:9983000-9984600	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr2:9983000-9984600	Active TSS	Gastric	stomach

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