Variant report

Variant	rs13003628
Chromosome Location	chr2:234777040-234777041
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:185)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:185 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELK1	chr2:234776874-234777173	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr2:234776806-234777136	K562	blood:	n/a	n/a
3	POLR2A	chr2:234776748-234777244	GM18505	blood:	n/a	n/a
4	BRCA1	chr2:234776797-234777276	Hela-S3	cervix:	n/a	n/a
5	MAX	chr2:234776509-234777363	A549	lung:	n/a	n/a
6	MYC	chr2:234776649-234777214	K562	blood:	n/a	n/a
7	TCF7L2	chr2:234776763-234777219	PANC-1	pancreas:	n/a	n/a
8	REST	chr2:234776747-234777060	PANC-1	pancreas:	n/a	n/a
9	E2F6	chr2:234776514-234777268	A549	lung:	n/a	n/a
10	ATF3	chr2:234776897-234777171	K562	blood:	n/a	n/a
11	CCNT2	chr2:234776803-234777122	K562	blood:	n/a	n/a
12	POLR2A	chr2:234776562-234777333	PFSK-1	brain:	n/a	n/a
13	CREB1	chr2:234776675-234777244	H1-hESC	embryonic stem cell:	n/a	n/a
14	HEY1	chr2:234776803-234777158	K562	blood:	n/a	chr2:234777091-234777106
15	POLR2A	chr2:234776622-234777245	MCF-7	breast:	n/a	n/a
16	POLR2A	chr2:234776660-234777185	PANC-1	pancreas:	n/a	n/a
17	MAX	chr2:234776727-234777151	Hela-S3	cervix:	n/a	n/a
18	CREB1	chr2:234776679-234777354	K562	blood:	n/a	n/a
19	SRF	chr2:234776879-234777163	H1-hESC	embryonic stem cell:	n/a	n/a
20	BCL3	chr2:234776610-234777061	A549	lung:	n/a	n/a
21	MXI1	chr2:234776951-234777203	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr2:234776725-234777128	K562	blood:	n/a	n/a
23	BACH1	chr2:234776867-234777055	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAX	chr2:234776570-234777155	K562	blood:	n/a	n/a
25	ELF1	chr2:234776650-234777186	GM12878	blood:	n/a	n/a
26	POLR2A	chr2:234776804-234777187	MCF10A-Er-Src	breast:	n/a	n/a
27	RUNX3	chr2:234776729-234777118	GM12878	blood:	n/a	n/a
28	POLR2A	chr2:234776679-234777187	K562	blood:	n/a	n/a
29	POLR2A	chr2:234776742-234777163	Hela-S3	cervix:	n/a	n/a
30	SRF	chr2:234776857-234777115	K562	blood:	n/a	n/a
31	POLR2A	chr2:234776746-234777175	PBDE	blood:	n/a	n/a
32	E2F4	chr2:234776999-234777221	MCF10A-Er-Src	breast:	n/a	n/a
33	TCF12	chr2:234776467-234777327	A549	lung:	n/a	n/a
34	E2F6	chr2:234776616-234777138	K562	blood:	n/a	n/a
35	POLR2A	chr2:234776667-234777171	H1-hESC	embryonic stem cell:	n/a	n/a
36	KAP1	chr2:234776802-234777081	U2OS	brain:	n/a	chr2:234776961-234776969
37	POLR2A	chr2:234776642-234777245	GM12891	blood:	n/a	n/a
38	POLR2A	chr2:234776652-234777251	HCT-116	colon:	n/a	n/a
39	TCF7L2	chr2:234776810-234777177	Hela-S3	cervix:	n/a	n/a
40	MAX	chr2:234776380-234777363	A549	lung:	n/a	n/a
41	TBP	chr2:234776944-234777262	Hela-S3	cervix:	n/a	n/a
42	ELF1	chr2:234776799-234777165	MCF-7	breast:	n/a	n/a
43	POLR2A	chr2:234776733-234777226	K562	blood:	n/a	n/a
44	CTCF	chr2:234776949-234777430	K562	blood:	n/a	n/a
45	GTF2F1	chr2:234776857-234777153	K562	blood:	n/a	n/a
46	POLR2A	chr2:234776774-234777134	GM12892	blood:	n/a	n/a
47	POLR2A	chr2:234776600-234777274	HCT-116	colon:	n/a	n/a
48	TCF12	chr2:234776768-234777199	ECC-1	luminal epithelium:	n/a	n/a
49	ZNF143	chr2:234776726-234777091	K562	blood:	n/a	n/a
50	IRF1	chr2:234776791-234777265	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:234775602..234777791-chr7:117824084..117825749,2	MCF-7	breast:
2	2:234635414-234639782..2:234772667-234780240	Hela-S3	cervix:
3	chr2:234600369..234602177-chr2:234775436..234777156,2	MCF-7	breast:
4	2:234683624-234705119..2:234772667-234780240	Hela-S3	cervix:
5	2:234772667-234780240..2:234954947-234965240	Hela-S3	cervix:
6	2:234543708-234558325..2:234772667-234780240	Hela-S3	cervix:

No data

Variant related genes	Relation type
MSL3P1	TF binding region
ENSG00000167165	Chromatin interaction
ENSG00000128534	Chromatin interaction
ENSG00000072080	Chromatin interaction
ENSG00000185038	Chromatin interaction
ENSG00000234143	Chromatin interaction
ENSG00000241635	Chromatin interaction
ENSG00000243135	Chromatin interaction
ENSG00000242515	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs169922	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs183331	0.95[EUR][1000 genomes]
rs213542	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs213545	0.91[EUR][1000 genomes]
rs2215172	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2302156	0.93[ASN][1000 genomes]
rs4663339	0.96[EUR][1000 genomes]
rs501145	0.94[ASN][1000 genomes]
rs525359	0.93[ASN][1000 genomes]
rs556691	0.93[ASN][1000 genomes]
rs580045	0.94[ASN][1000 genomes]
rs619929	0.90[ASN][1000 genomes]
rs626110	0.92[ASN][1000 genomes]
rs637082	0.93[ASN][1000 genomes]
rs638071	0.91[ASN][1000 genomes]
rs6431643	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6431644	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs650570	0.92[ASN][1000 genomes]
rs650700	0.93[ASN][1000 genomes]
rs654279	0.93[ASN][1000 genomes]
rs7596657	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers 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	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234775200-234777400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:234775600-234777200	Active TSS	Hela-S3	cervix
3	chr2:234776000-234777400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:234776000-234777400	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr2:234776000-234777400	Active TSS	A549	lung
6	chr2:234776000-234777400	Active TSS	K562	blood
7	chr2:234776200-234777400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:234776400-234777200	Active TSS	H1 Cell Line	embryonic stem cell
9	chr2:234776400-234777200	Active TSS	H9 Cell Line	embryonic stem cell
10	chr2:234776400-234777200	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr2:234776400-234777200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:234776400-234777400	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr2:234776400-234777400	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr2:234776400-234777400	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr2:234776400-234777400	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr2:234776400-234777400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr2:234776400-234777400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:234776400-234777400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:234776400-234777600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:234776400-234777600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:234776400-234777600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:234776600-234777200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:234776600-234777200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:234776600-234777200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:234776600-234777200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr2:234776600-234777200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:234776600-234777200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:234776600-234777200	Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr2:234776600-234777200	Active TSS	Brain Angular Gyrus	brain
30	chr2:234776600-234777200	Active TSS	Brain Cingulate Gyrus	brain
31	chr2:234776600-234777200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:234776600-234777200	Active TSS	Brain Substantia Nigra	brain
33	chr2:234776600-234777200	Active TSS	Colonic Mucosa	Colon
34	chr2:234776600-234777200	Active TSS	Colon Smooth Muscle	Colon
35	chr2:234776600-234777200	Bivalent/Poised TSS	Left Ventricle	heart
36	chr2:234776600-234777200	Bivalent/Poised TSS	Psoas Muscle	Psoas
37	chr2:234776600-234777200	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr2:234776600-234777200	Active TSS	Rectal Smooth Muscle	rectum
39	chr2:234776600-234777200	Active TSS	Right Ventricle	heart
40	chr2:234776600-234777200	Active TSS	Stomach Mucosa	stomach
41	chr2:234776600-234777200	Active TSS	Thymus	Thymus
42	chr2:234776600-234777200	Active TSS	NHEK	skin
43	chr2:234776600-234777200	Active TSS	Osteobl	bone
44	chr2:234776600-234777400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:234776600-234777400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr2:234776600-234777400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:234776600-234777400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr2:234776600-234777400	Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr2:234776600-234777400	Active TSS	Muscle Satellite Cultured Cells	--
50	chr2:234776600-234777400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain

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