Variant report

Variant	rs6725228
Chromosome Location	chr2:113398889-113398890
allele	A/G
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	NR2F2	chr2:113398104-113399134	K562	blood:	n/a	n/a
2	MYC	chr2:113398462-113398949	MCF10A-Er-Src	breast:	n/a	n/a
3	JUND	chr2:113398280-113399218	K562	blood:	n/a	chr2:113398544-113398551 chr2:113398542-113398553 chr2:113398740-113398750 chr2:113398543-113398552
4	ZNF263	chr2:113398203-113399110	HEK293-T-REx	kidney:	n/a	chr2:113398506-113398527
5	RCOR1	chr2:113398321-113399291	K562	blood:	n/a	n/a
6	EGR1	chr2:113398016-113398987	HCT-116	colon:	n/a	chr2:113398558-113398571
7	MAX	chr2:113398297-113399601	K562	blood:	n/a	chr2:113399438-113399448
8	EP300	chr2:113398392-113399216	K562	blood:	n/a	n/a
9	NFIC	chr2:113397920-113399223	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr2:113397694-113399879	U87	brain:	n/a	n/a
11	MAX	chr2:113398390-113399608	NB4	blood:	n/a	chr2:113399438-113399448
12	FOS	chr2:113398305-113398959	HUVEC	blood vessel:	n/a	chr2:113398544-113398551 chr2:113398740-113398750 chr2:113398543-113398552 chr2:113398542-113398553
13	RCOR1	chr2:113397515-113399670	IMR90	lung:	n/a	n/a
14	MYC	chr2:113398476-113398907	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr2:113398270-113399118	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr2:113397844-113399679	U87	brain:	n/a	n/a
17	JUND	chr2:113397464-113399400	SK-N-SH	brain:	n/a	chr2:113398544-113398551 chr2:113398542-113398553 chr2:113398740-113398750 chr2:113398543-113398552
18	EGR1	chr2:113398211-113398951	HCT-116	colon:	n/a	chr2:113398558-113398571
19	FOSL1	chr2:113398112-113399055	HCT-116	colon:	n/a	chr2:113398544-113398551 chr2:113398542-113398553 chr2:113398740-113398750 chr2:113398543-113398552
20	MAX	chr2:113398306-113399131	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr2:113398813-113399273	K562	blood:	n/a	n/a
22	EP300	chr2:113397900-113399282	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr2:113398176-113399428	HUVEC	blood vessel:	n/a	n/a
24	JUN	chr2:113398110-113399563	K562	blood:	n/a	chr2:113398544-113398551 chr2:113398740-113398750 chr2:113398543-113398552
25	FOSL2	chr2:113397527-113398941	SK-N-SH	brain:	n/a	chr2:113398544-113398551 chr2:113398740-113398750 chr2:113398543-113398552
26	POLR2A	chr2:113398104-113398969	PFSK-1	brain:	n/a	n/a
27	EGR1	chr2:113398750-113399052	K562	blood:	n/a	n/a
28	POLR2A	chr2:113398878-113399183	K562	blood:	n/a	n/a
29	POLR2A	chr2:113397940-113398974	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr2:113397976-113399510	U87	brain:	n/a	n/a
31	PBX3	chr2:113397970-113398926	SK-N-SH	brain:	n/a	n/a
32	TCF12	chr2:113397911-113398967	SK-N-SH	brain:	n/a	chr2:113398811-113398818 chr2:113398555-113398565
33	TCF12	chr2:113397903-113399358	SK-N-SH	brain:	n/a	chr2:113398811-113398818 chr2:113398555-113398565
34	HEY1	chr2:113398323-113399106	K562	blood:	n/a	n/a
35	TEAD4	chr2:113398205-113399052	K562	blood:	n/a	n/a
36	POLR2A	chr2:113397872-113399688	IMR90	lung:	n/a	n/a
37	ZNF263	chr2:113398158-113399177	K562	blood:	n/a	chr2:113398506-113398527
38	MYC	chr2:113398383-113399074	NB4	blood:	n/a	n/a
39	JUND	chr2:113397987-113398894	SK-N-SH	brain:	n/a	chr2:113398544-113398551 chr2:113398542-113398553 chr2:113398740-113398750 chr2:113398543-113398552
40	POLR2A	chr2:113397952-113399051	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:113379636..113386577-chr2:113398111..113406278,16	MCF-7	breast:
2	chr2:113398028..113400267-chr2:113464007..113465534,2	K562	blood:
3	chr2:113396800..113399610-chr2:113484528..113487337,2	MCF-7	breast:

Variant related genes	Relation type
SLC20A1	TF binding region
ENSG00000144130	Chromatin interaction
ENSG00000231747	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10171024	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10184339	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10758	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12612089	0.86[EUR][1000 genomes]
rs17515708	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17515715	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2048873	0.85[EUR][1000 genomes]
rs34282612	0.86[ASN][1000 genomes]
rs35048989	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3827758	0.81[ASN][1000 genomes]
rs4849086	0.93[EUR][1000 genomes]
rs4849091	0.93[ASN][1000 genomes]
rs57033895	0.87[ASN][1000 genomes]
rs58662040	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58797970	0.85[ASN][1000 genomes]
rs60372418	0.86[EUR][1000 genomes]
rs6542074	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv470480	chr2:113373950-113429752	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv1010106	chr2:113394981-113556071	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113385000-113402600	Weak transcription	Esophagus	oesophagus
2	chr2:113385800-113401800	Weak transcription	Brain Hippocampus Middle	brain
3	chr2:113389400-113402000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:113389600-113402200	Weak transcription	Primary B cells from cord blood	blood
5	chr2:113389800-113400400	Weak transcription	Fetal Intestine Small	intestine
6	chr2:113392800-113402000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:113394400-113402000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr2:113394600-113402000	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:113394800-113402000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr2:113395000-113400200	Weak transcription	Primary T cells from cord blood	blood
11	chr2:113395000-113401400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr2:113395000-113402000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr2:113395200-113401800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr2:113395600-113400800	Weak transcription	Liver	Liver
15	chr2:113396800-113399200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:113396800-113400400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:113397000-113401800	Enhancers	HMEC	breast
18	chr2:113397200-113402000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:113397400-113401600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr2:113397600-113399200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:113397600-113399400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:113397600-113399600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:113397600-113402200	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr2:113397800-113399200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:113397800-113399200	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr2:113397800-113399200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:113397800-113399200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:113397800-113399200	Flanking Active TSS	Osteobl	bone
29	chr2:113397800-113399400	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr2:113397800-113399400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr2:113397800-113399600	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr2:113397800-113399600	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr2:113397800-113399800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:113398000-113399000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:113398000-113399000	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr2:113398000-113399000	Flanking Active TSS	NH-A	brain
37	chr2:113398000-113399200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr2:113398000-113399200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:113398000-113399200	Enhancers	Colonic Mucosa	Colon
40	chr2:113398000-113399200	Enhancers	Hela-S3	cervix
41	chr2:113398000-113399600	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr2:113398000-113399800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:113398000-113400400	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr2:113398000-113401600	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr2:113398000-113402000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:113398200-113399000	Flanking Active TSS	NHEK	skin
47	chr2:113398200-113399200	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr2:113398200-113399200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:113398200-113399200	Enhancers	Fetal Muscle Trunk	muscle
50	chr2:113398200-113399200	Enhancers	Lung	lung

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