Variant report

Variant	rs2288558
Chromosome Location	chr7:128117343-128117344
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	POLR2A	chr7:128116468-128117385	MCF-7	breast:	n/a	n/a
2	SIN3AK20	chr7:128116520-128117449	K562	blood:	n/a	n/a
3	UBTF	chr7:128116466-128117436	K562	blood:	n/a	n/a
4	CTCF	chr7:128116432-128117448	K562	blood:	n/a	n/a
5	CTCF	chr7:128117200-128117350	SK-N-SH_RA	brain:	n/a	n/a
6	HEY1	chr7:128116288-128117446	K562	blood:	n/a	n/a
7	MXI1	chr7:128116227-128117779	IMR90	lung:	n/a	n/a
8	POLR2A	chr7:128116386-128117466	K562	blood:	n/a	n/a
9	TAF1	chr7:128116339-128117412	A549	lung:	n/a	n/a
10	RUNX3	chr7:128116568-128117482	GM12878	blood:	n/a	n/a
11	MXI1	chr7:128116167-128117916	SK-N-SH	brain:	n/a	n/a
12	SIN3AK20	chr7:128116459-128117355	SK-N-SH	brain:	n/a	n/a
13	RCOR1	chr7:128117305-128117404	K562	blood:	n/a	n/a
14	TAF1	chr7:128116412-128117411	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr7:128117220-128117370	HMEC	breast:	n/a	n/a
16	HCFC1	chr7:128116301-128117565	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr7:128116324-128117423	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr7:128116495-128117437	GM15510	blood:	n/a	n/a
19	NFATC1	chr7:128117277-128117798	GM12878	blood:	n/a	chr7:128117586-128117599
20	ELF1	chr7:128117222-128117416	K562	blood:	n/a	n/a
21	POLR2A	chr7:128116460-128117368	GM12878	blood:	n/a	n/a
22	HA-E2F1	chr7:128116325-128117491	MCF-7	breast:	n/a	chr7:128116711-128116723 chr7:128116726-128116738 chr7:128116727-128116734 chr7:128116727-128116734 chr7:128116722-128116737 chr7:128116727-128116734 chr7:128116726-128116737 chr7:128116723-128116737 chr7:128116726-128116735
23	POLR2A	chr7:128116294-128117422	MCF10A-Er-Src	breast:	n/a	n/a
24	FOXM1	chr7:128116493-128117536	GM12878	blood:	n/a	n/a
25	POLR2A	chr7:128116287-128117409	GM12878	blood:	n/a	n/a
26	EGR1	chr7:128117161-128117448	K562	blood:	n/a	n/a
27	NFATC1	chr7:128117326-128117788	GM12878	blood:	n/a	chr7:128117586-128117599
28	POLR2A	chr7:128117115-128117387	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAX	chr7:128116496-128117423	Hela-S3	cervix:	n/a	chr7:128116610-128116620
30	POLR2A	chr7:128116324-128117436	K562	blood:	n/a	n/a
31	POLR2A	chr7:128116243-128117446	GM12892	blood:	n/a	n/a
32	TRIM28	chr7:128116257-128117749	K562	blood:	n/a	n/a
33	TAF1	chr7:128116462-128117356	HepG2	liver:	n/a	n/a
34	YY1	chr7:128116437-128117406	A549	lung:	n/a	n/a
35	POLR2A	chr7:128116394-128117359	Hela-S3	cervix:	n/a	n/a
36	MAX	chr7:128117158-128117422	K562	blood:	n/a	n/a
37	CBX3	chr7:128116163-128117737	K562	blood:	n/a	n/a
38	POLR2A	chr7:128116458-128117393	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr7:128116328-128117762	PBDE	blood:	n/a	n/a
40	TAF1	chr7:128116312-128117512	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr7:128117220-128117370	GM12870	blood:	n/a	n/a
42	TAF1	chr7:128117214-128117413	K562	blood:	n/a	n/a
43	POLR2A	chr7:128116387-128117422	H1-hESC	embryonic stem cell:	n/a	n/a
44	MAX	chr7:128117166-128117436	K562	blood:	n/a	n/a
45	POLR2A	chr7:128116346-128117378	GM12878	blood:	n/a	n/a
46	POLR2A	chr7:128116460-128117376	GM12878	blood:	n/a	n/a
47	TEAD4	chr7:128116225-128117373	K562	blood:	n/a	chr7:128116528-128116537
48	IRF4	chr7:128116571-128117350	GM12878	blood:	n/a	n/a
49	FOXM1	chr7:128116493-128117399	GM12878	blood:	n/a	n/a
50	STAT5A	chr7:128116266-128117479	K562	blood:	n/a	chr7:128117365-128117377

No.	Distal block	Cell Line	Cell type
1	chr7:128049014..128051472-chr7:128115731..128117859,3	K562	blood:
2	chr7:128115173..128117389-chr7:128298817..128301721,2	K562	blood:
3	chr7:128094286..128097516-chr7:128115288..128118444,4	K562	blood:
4	chr7:128116092..128118343-chr7:128171049..128172892,4	K562	blood:
5	chr17:16118309..16118871-chr7:128116620..128117465,2	Hela-S3	cervix:
6	chr7:128116465..128119803-chr7:128169321..128173196,4	MCF-7	breast:

Variant related genes	Relation type
METTL2B	TF binding region
ENSG00000141027	Chromatin interaction
ENSG00000242588	Chromatin interaction
ENSG00000273184	Chromatin interaction
ENSG00000240758	Chromatin interaction
ENSG00000273270	Chromatin interaction
ENSG00000271529	Chromatin interaction
ENSG00000106348	Chromatin interaction
ENSG00000135245	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2288551	0.92[AMR][1000 genomes]
rs2288552	0.92[AMR][1000 genomes]
rs2288555	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34742251	0.83[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap]
rs3793166	1.00[AMR][1000 genomes]
rs3802002	1.00[AFR][1000 genomes]
rs56777177	1.00[AMR][1000 genomes]
rs57025636	0.87[ASN][1000 genomes]
rs57342587	0.86[ASN][1000 genomes]
rs58116488	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs58306387	0.86[ASN][1000 genomes]
rs58346994	0.86[ASN][1000 genomes]
rs58432768	0.86[ASN][1000 genomes]
rs59521761	0.86[ASN][1000 genomes]
rs59959624	0.86[ASN][1000 genomes]
rs61030579	0.86[ASN][1000 genomes]
rs714510	0.81[CHB][hapmap]
rs72624929	0.92[AMR][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	nsv831124	chr7:127970345-128147910	Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv966883	chr7:128107081-128142581	Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 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	chr7:128116200-128117400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
2	chr7:128116200-128117400	Active TSS	Fetal Brain Female	brain
3	chr7:128116200-128117400	Active TSS	Osteobl	bone
4	chr7:128116200-128117600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:128116200-128117600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:128116200-128117600	Active TSS	Brain Angular Gyrus	brain
7	chr7:128116200-128117600	Active TSS	Fetal Muscle Trunk	muscle
8	chr7:128116200-128117600	Active TSS	Left Ventricle	heart
9	chr7:128116200-128117600	Active TSS	Right Ventricle	heart
10	chr7:128116200-128117800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr7:128116200-128117800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:128116200-128118000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:128116200-128118000	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr7:128116200-128118000	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr7:128116200-128118000	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr7:128116200-128118000	Active TSS	Brain Germinal Matrix	brain
17	chr7:128116200-128118000	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr7:128116200-128118200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr7:128116400-128117400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr7:128116400-128117400	Active TSS	Aorta	Aorta
21	chr7:128116400-128117400	Active TSS	Liver	Liver
22	chr7:128116400-128117400	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr7:128116400-128117400	Active TSS	Pancreas	Pancrea
24	chr7:128116400-128117400	Active TSS	Placenta Amnion	Placenta Amnion
25	chr7:128116400-128117400	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr7:128116400-128117400	Active TSS	Thymus	Thymus
27	chr7:128116400-128117400	Active TSS	HSMMtube	muscle
28	chr7:128116400-128117600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr7:128116400-128117600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
30	chr7:128116400-128117600	Active TSS	Brain Substantia Nigra	brain
31	chr7:128116400-128117600	Active TSS	Fetal Stomach	stomach
32	chr7:128116400-128117600	Active TSS	Fetal Thymus	thymus
33	chr7:128116400-128117600	Active TSS	Ovary	ovary
34	chr7:128116400-128117600	Active TSS	Rectal Smooth Muscle	rectum
35	chr7:128116400-128117600	Active TSS	Stomach Smooth Muscle	stomach
36	chr7:128116400-128117600	Active TSS	NH-A	brain
37	chr7:128116400-128117800	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr7:128116400-128117800	Active TSS	H9 Cell Line	embryonic stem cell
39	chr7:128116400-128117800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr7:128116400-128117800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr7:128116400-128117800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr7:128116400-128117800	Active TSS	Psoas Muscle	Psoas
43	chr7:128116400-128117800	Active TSS	NHLF	lung
44	chr7:128116400-128118000	Active TSS	H1 Cell Line	embryonic stem cell
45	chr7:128116400-128118000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr7:128116400-128118000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr7:128116400-128118000	Active TSS	Colonic Mucosa	Colon
48	chr7:128116400-128118000	Active TSS	Fetal Intestine Large	intestine
49	chr7:128116400-128118200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr7:128116600-128117400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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