Variant report

Variant	rs6576989
Chromosome Location	chr2:97525099-97525100
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:96)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:96 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PML	chr2:97524449-97525499	K562	blood:	n/a	n/a
2	POLR2A	chr2:97524801-97525456	K562	blood:	n/a	n/a
3	ELK1	chr2:97525048-97525160	K562	blood:	n/a	n/a
4	MTA3	chr2:97525080-97525429	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:97524446-97525180	ProgFib	skin:	n/a	n/a
6	PML	chr2:97524379-97525494	MCF-7	breast:	n/a	n/a
7	CCNT2	chr2:97522969-97525445	K562	blood:	n/a	n/a
8	POLR2A	chr2:97524475-97525306	H1-neurons	neurons:	n/a	n/a
9	HMGN3	chr2:97522921-97525401	K562	blood:	n/a	n/a
10	POLR2A	chr2:97524772-97525293	GM12891	blood:	n/a	n/a
11	POLR2A	chr2:97522659-97525626	SK-N-MC	brain:	n/a	n/a
12	POLR2A	chr2:97524768-97525424	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr2:97524471-97526443	K562	blood:	n/a	n/a
14	NFATC1	chr2:97524500-97525276	GM12878	blood:	n/a	n/a
15	JUND	chr2:97525007-97525215	H1-hESC	embryonic stem cell:	n/a	n/a
16	CHD2	chr2:97524534-97525526	K562	blood:	n/a	n/a
17	SIN3AK20	chr2:97522597-97525448	MCF-7	breast:	n/a	n/a
18	POLR2A	chr2:97524972-97525273	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr2:97524462-97525688	GM12891	blood:	n/a	n/a
20	ZMIZ1	chr2:97524494-97525258	K562	blood:	n/a	n/a
21	MTA3	chr2:97523360-97525490	GM12878	blood:	n/a	n/a
22	EP300	chr2:97524894-97525294	K562	blood:	n/a	n/a
23	POLR2A	chr2:97524786-97525397	GM12878	blood:	n/a	n/a
24	POLR2A	chr2:97524665-97526140	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr2:97524528-97525461	K562	blood:	n/a	n/a
26	POLR2A	chr2:97522747-97525500	GM12892	blood:	n/a	n/a
27	POLR2A	chr2:97524430-97525477	GM12892	blood:	n/a	n/a
28	EBF1	chr2:97525051-97525482	GM12878	blood:	n/a	chr2:97525247-97525258 chr2:97525246-97525259
29	ELF1	chr2:97522793-97525207	GM12878	blood:	n/a	chr2:97523391-97523404
30	MXI1	chr2:97522753-97525131	IMR90	lung:	n/a	chr2:97524626-97524635
31	POLR2A	chr2:97522785-97526347	HepG2	liver:	n/a	n/a
32	POLR2A	chr2:97523607-97528252	K562	blood:	n/a	n/a
33	POLR2A	chr2:97524427-97525496	PANC-1	pancreas:	n/a	n/a
34	POLR2A	chr2:97524429-97525448	ECC-1	luminal epithelium:	n/a	n/a
35	STAT5A	chr2:97524418-97525515	GM12878	blood:	n/a	chr2:97525159-97525167
36	POLR2A	chr2:97524637-97525666	MCF10A-Er-Src	breast:	n/a	n/a
37	RUNX3	chr2:97525063-97525519	GM12878	blood:	n/a	n/a
38	POLR2A	chr2:97524650-97525503	GM12892	blood:	n/a	n/a
39	POLR2A	chr2:97524450-97525709	HepG2	liver:	n/a	n/a
40	POLR2A	chr2:97524477-97526345	MCF10A-Er-Src	breast:	n/a	n/a
41	RAD21	chr2:97524445-97525128	H1-hESC	embryonic stem cell:	n/a	chr2:97524661-97524674
42	TEAD4	chr2:97524371-97525494	K562	blood:	n/a	n/a
43	MAZ	chr2:97522796-97525574	K562	blood:	n/a	chr2:97523561-97523570 chr2:97524172-97524181
44	POLR2A	chr2:97524428-97525519	K562	blood:	n/a	n/a
45	POLR2A	chr2:97524385-97525453	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr2:97523482-97526772	K562	blood:	n/a	n/a
47	POLR2A	chr2:97524445-97525730	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr2:97524780-97525314	GM12892	blood:	n/a	n/a
49	POLR2A	chr2:97522812-97526819	HepG2	liver:	n/a	n/a
50	BHLHE40	chr2:97524564-97525246	K562	blood:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:97524495..97526579-chr2:97610763..97613644,2	K562	blood:
2	chr2:97516728..97547486-chr2:97588377..97628331,265	MCF-7	breast:
3	chr2:97522291..97526078-chr2:97561305..97564829,3	K562	blood:
4	chr2:97481330..97483685-chr2:97521136..97525158,3	K562	blood:
5	chr2:97503321..97507604-chr2:97523839..97527603,4	K562	blood:
6	chr2:97524151..97526092-chr2:97601214..97603096,2	K562	blood:
7	chr2:97509315..97510940-chr2:97523525..97525139,2	MCF-7	breast:
8	chr2:97503321..97506022-chr2:97524781..97527603,2	K562	blood:
9	chr2:97488123..97491381-chr2:97522097..97525123,6	MCF-7	breast:
10	chr2:97483756..97486105-chr2:97524140..97526668,2	K562	blood:
11	chr2:97523891..97526324-chr2:97628583..97631770,4	MCF-7	breast:
12	chr2:97523665..97525724-chr2:97777402..97779360,2	MCF-7	breast:
13	chr2:97524163..97526648-chr2:97606538..97609539,3	K562	blood:
14	chr2:97481330..97485256-chr2:97521136..97525640,5	K562	blood:
15	chr2:97521500..97526453-chr2:97614513..97620136,8	K562	blood:
16	chr2:97524151..97525975-chr2:97600172..97602714,2	K562	blood:
17	chr2:97521500..97526547-chr2:97614513..97619168,8	K562	blood:

No data

Variant related genes	Relation type
ANKRD23	TF binding region
ANKRD39	TF binding region
ENSG00000252845	Chromatin interaction
ENSG00000168763	Chromatin interaction
ENSG00000135976	Chromatin interaction
ENSG00000163126	Chromatin interaction
ENSG00000168754	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10203346	0.86[EUR][1000 genomes]
rs10439526	0.84[EUR][1000 genomes]
rs11897786	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12172	0.82[EUR][1000 genomes]
rs12846	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1317911	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1320146	0.88[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs1320149	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13419073	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17119598	0.88[MEX][hapmap]
rs2276654	0.88[MEX][hapmap]
rs3731941	0.88[MEX][hapmap]
rs55674661	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58147284	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59244622	0.82[EUR][1000 genomes]
rs62152795	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62152834	0.84[EUR][1000 genomes]
rs62152860	0.86[EUR][1000 genomes]
rs62152863	0.87[EUR][1000 genomes]
rs62152864	0.87[EUR][1000 genomes]
rs6576986	0.87[EUR][1000 genomes]
rs6576987	0.88[MEX][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs6753987	0.88[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72811623	0.84[EUR][1000 genomes]
rs72811629	0.84[EUR][1000 genomes]
rs7580942	1.00[MEX][hapmap];0.89[TSI][hapmap]
rs7594727	1.00[ASW][hapmap];0.88[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7608621	1.00[ASW][hapmap];0.88[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9948	0.88[MEX][hapmap];0.89[TSI][hapmap]
rs9973492	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6576989	FAHD2CP	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97522400-97525200	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr2:97522600-97525200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr2:97523000-97525200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr2:97523200-97525200	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr2:97523800-97533000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:97524200-97525600	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr2:97524200-97525800	Weak transcription	Aorta	Aorta
8	chr2:97524200-97526200	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr2:97524200-97526200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:97524200-97526400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:97524200-97526600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:97524200-97533400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:97524400-97525200	Flanking Active TSS	Brain Germinal Matrix	brain
14	chr2:97524400-97525400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:97524400-97525400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr2:97524400-97525800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:97524400-97525800	Weak transcription	NHEK	skin
18	chr2:97524400-97525800	Enhancers	NHLF	lung
19	chr2:97524400-97529600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr2:97524600-97525200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:97524600-97525200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:97524600-97525200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:97524600-97525200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr2:97524600-97525200	Flanking Active TSS	Rectal Smooth Muscle	rectum
25	chr2:97524600-97525200	Enhancers	Right Atrium	heart
26	chr2:97524600-97525200	Enhancers	Stomach Mucosa	stomach
27	chr2:97524600-97525200	Enhancers	NH-A	brain
28	chr2:97524600-97525400	Flanking Active TSS	Brain Substantia Nigra	brain
29	chr2:97524600-97525400	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr2:97524600-97525600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:97524600-97525600	Enhancers	Placenta Amnion	Placenta Amnion
32	chr2:97524600-97525800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:97524600-97525800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:97524600-97525800	Enhancers	Fetal Muscle Leg	muscle
35	chr2:97524600-97526000	Enhancers	Primary T cells fromperipheralblood	blood
36	chr2:97524600-97526000	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr2:97524600-97526000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr2:97524600-97526000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:97524600-97526000	Enhancers	Liver	Liver
40	chr2:97524600-97526000	Enhancers	Left Ventricle	heart
41	chr2:97524600-97526000	Weak transcription	Ovary	ovary
42	chr2:97524600-97526200	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr2:97524600-97526200	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr2:97524600-97526400	Enhancers	Primary T cells from cord blood	blood
45	chr2:97524600-97526400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr2:97524600-97526400	Enhancers	Fetal Brain Male	brain
47	chr2:97524600-97526400	Enhancers	Fetal Thymus	thymus
48	chr2:97524600-97526600	Enhancers	Fetal Heart	heart
49	chr2:97524600-97527600	Weak transcription	GM12878-XiMat	blood
50	chr2:97524600-97527800	Weak transcription	Fetal Kidney	kidney

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