Variant report

Variant	rs2579501
Chromosome Location	chr2:97199251-97199252
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:97199056-97199787	HL-60	blood:	n/a	n/a
2	MAZ	chr2:97199091-97199711	Hela-S3	cervix:	n/a	n/a
3	ZKSCAN1	chr2:97198590-97199639	Hela-S3	cervix:	n/a	n/a
4	TFAP2C	chr2:97198885-97199914	Hela-S3	cervix:	n/a	n/a
5	TCF7L2	chr2:97199216-97199855	Hela-S3	cervix:	n/a	chr2:97199579-97199586
6	EBF1	chr2:97198802-97199831	GM12878	blood:	n/a	chr2:97199024-97199034 chr2:97199024-97199033 chr2:97199021-97199032
7	POLR2A	chr2:97198966-97199754	HL-60	blood:	n/a	n/a
8	MAX	chr2:97199109-97199699	Hela-S3	cervix:	n/a	n/a
9	EP300	chr2:97199227-97199424	GM12878	blood:	n/a	n/a
10	MYC	chr2:97199205-97199846	MCF10A-Er-Src	breast:	n/a	n/a
11	SPI1	chr2:97199032-97199817	HL-60	blood:	n/a	n/a
12	MAX	chr2:97199237-97199306	GM12878	blood:	n/a	n/a
13	TFAP2A	chr2:97199138-97199925	Hela-S3	cervix:	n/a	chr2:97199664-97199679
14	SMARCC1	chr2:97197223-97199574	Hela-S3	cervix:	n/a	n/a
15	STAT3	chr2:97199247-97199817	MCF10A-Er-Src	breast:	n/a	chr2:97199281-97199289

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:97199248-97199298	NH-A	brain:	n/a
2	chr2:97199248-97199298	HRPEpiC	eye:	n/a
3	chr2:97199248-97199298	AG09309	skin:	n/a
4	chr2:97199248-97199298	NHDF-neo	bronchial:	n/a
5	chr2:97199248-97199298	MCF-7	breast:	n/a
6	chr2:97199248-97199298	PFSK-1	brain:	n/a
7	chr2:97199248-97199298	Hela-S3	cervix:	n/a
8	chr2:97199248-97199298	AG04450	lung:	fetal
9	chr2:97199248-97199298	PANC-1	pancreas:	n/a
10	chr2:97199248-97199298	K562	blood:	n/a
11	chr2:97199248-97199298	BE2_C	brain:	n/a
12	chr2:97199248-97199298	Jurkat	blood:	n/a
13	chr2:97199248-97199298	SK-N-SH	brain:	n/a
14	chr2:97199248-97199298	RPTEC	kidney:	n/a
15	chr2:97199248-97199298	AG09319	gingival:	n/a
16	chr2:97199248-97199298	HL-60	blood:	n/a
17	chr2:97199248-97199298	SK-N-SH_RA	brain:	n/a
18	chr2:97199248-97199298	HepG2	liver:	n/a
19	chr2:97199248-97199298	HMEC	breast:	n/a
20	chr2:97199248-97199298	MCF10A-Er-Src	breast:	n/a
21	chr2:97199248-97199298	U87	brain:	n/a
22	chr2:97199248-97199298	ProgFib	skin:	n/a
23	chr2:97199248-97199298	HCT-116	colon:	n/a
24	chr2:97199248-97199298	HCM	heart:	n/a
25	chr2:97199248-97199298	ECC-1	luminal epithelium:	n/a
26	chr2:97199248-97199298	SKMC	muscle:	n/a
27	chr2:97199248-97199298	Caco-2	colon:	n/a
28	chr2:97199248-97199298	HEEpiC	esophagus:	n/a
29	chr2:97199248-97199298	NB4	blood:	n/a
30	chr2:97199248-97199298	LNCaP	prostate:	n/a
31	chr2:97199248-97199298	A549	lung:	n/a
32	chr2:97199248-97199298	HIPEpiC	eye:	n/a
33	chr2:97199248-97199298	HAEpiC	amniotic membrane:	n/a
34	chr2:97199248-97199298	HCF	heart:	n/a
35	chr2:97199248-97199298	HCPEpiC	choroid plexus:	n/a
36	chr2:97199248-97199298	AG04449	skin:	fetal
37	chr2:97199248-97199298	Hepatocyte	liver:	n/a
38	chr2:97199248-97199298	HEK293	kidney:	embryo
39	chr2:97199248-97199298	IMR90	lung:	fetal
40	chr2:97199248-97199298	HRE	kidney:	n/a
41	chr2:97199248-97199298	GM12892	blood:	n/a
42	chr2:97199248-97199298	AG10803	skin:	n/a
43	chr2:97199248-97199298	SAEC	small airway:	n/a
44	chr2:97199248-97199298	H1-hESC	embryonic stem cell:	embryo
45	chr2:97199248-97199298	CMK	blood:	n/a
46	chr2:97199248-97199298	GM19239	blood:	n/a
47	chr2:97199248-97199298	GM12891	blood:	n/a
48	chr2:97199248-97199298	GM12878	blood:	n/a
49	chr2:97199248-97199298	ovcar-3	ovarian:	n/a
50	chr2:97199248-97199298	SK-N-MC	brain:	n/a

No data

Variant related genes	Relation type
ARID5A	TF binding region
ENSG00000235480	TF binding region
ARID5A	CpG island
ENSG00000235480	CpG island

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10177168	0.85[EUR][1000 genomes]
rs11676886	0.91[CEU][hapmap];0.83[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11891926	1.00[ASW][hapmap];0.91[CEU][hapmap];0.91[GIH][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap]
rs17634791	0.83[GIH][hapmap];0.88[TSI][hapmap]
rs1866444	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2438712	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2579498	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2579503	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2579506	0.87[CEU][hapmap]
rs2708975	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4907200	1.00[ASW][hapmap];0.91[CEU][hapmap];0.83[CHB][hapmap];0.91[GIH][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap]
rs56092602	0.81[EUR][1000 genomes]
rs6576974	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6576976	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6576978	1.00[ASW][hapmap];0.91[CEU][hapmap];0.83[CHB][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs6741277	1.00[ASW][hapmap];0.91[CEU][hapmap];0.83[CHB][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs6753926	0.82[EUR][1000 genomes]
rs7584930	0.91[CEU][hapmap];0.83[CHB][hapmap];0.83[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	esv3460902	chr2:97138421-97459342	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	esv3460903	chr2:97138421-97459342	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	nsv999871	chr2:97157196-97407711	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv535829	chr2:97157196-97407711	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2579501	TMEM127	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97193200-97201000	Enhancers	NHDF-Ad	bronchial
2	chr2:97194000-97202600	Enhancers	Placenta	Placenta
3	chr2:97194400-97202400	Enhancers	Lung	lung
4	chr2:97194800-97202000	Weak transcription	Liver	Liver
5	chr2:97195200-97199600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:97196200-97200800	Enhancers	NHLF	lung
7	chr2:97196800-97199600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:97197000-97201800	Enhancers	HSMMtube	muscle
9	chr2:97197200-97199400	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr2:97197200-97199600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:97197200-97199800	Enhancers	Spleen	Spleen
12	chr2:97197200-97200400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr2:97197200-97200600	Enhancers	Fetal Lung	lung
14	chr2:97197200-97200600	Enhancers	Stomach Mucosa	stomach
15	chr2:97197200-97202400	Enhancers	Brain Angular Gyrus	brain
16	chr2:97197200-97202400	Enhancers	Gastric	stomach
17	chr2:97197400-97200000	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr2:97197400-97200000	Enhancers	A549	lung
19	chr2:97197400-97202400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:97197400-97202400	Enhancers	Psoas Muscle	Psoas
21	chr2:97197600-97199800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:97197800-97199400	Enhancers	Esophagus	oesophagus
23	chr2:97197800-97199600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:97197800-97200400	Enhancers	Osteobl	bone
25	chr2:97197800-97200600	Enhancers	Primary hematopoietic stem cells	blood
26	chr2:97197800-97202000	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr2:97197800-97202400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr2:97198000-97199400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr2:97198000-97199400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr2:97198000-97199600	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr2:97198000-97199600	Enhancers	NH-A	brain
32	chr2:97198000-97199800	Enhancers	Primary B cells from peripheral blood	blood
33	chr2:97198000-97199800	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr2:97198000-97199800	Enhancers	Fetal Heart	heart
35	chr2:97198000-97199800	Enhancers	Fetal Thymus	thymus
36	chr2:97198000-97200000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:97198000-97200000	Enhancers	Muscle Satellite Cultured Cells	--
38	chr2:97198000-97200200	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr2:97198000-97200600	Enhancers	Right Atrium	heart
40	chr2:97198000-97200800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:97198000-97200800	Enhancers	Brain Cingulate Gyrus	brain
42	chr2:97198000-97201000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:97198000-97201000	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr2:97198000-97201000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:97198000-97201000	Enhancers	Brain Hippocampus Middle	brain
46	chr2:97198000-97201000	Enhancers	Fetal Stomach	stomach
47	chr2:97198000-97201200	Enhancers	Fetal Muscle Trunk	muscle
48	chr2:97198000-97202000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:97198000-97202000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:97198000-97202000	Enhancers	Adipose Nuclei	Adipose

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