Variant report

Variant	rs2225788
Chromosome Location	chr1:241681320-241681321
allele	G/T
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	EP300	chr1:241681280-241681435	GM12878	blood:	n/a	n/a
2	MXI1	chr1:241681252-241683457	IMR90	lung:	n/a	n/a
3	POLR2A	chr1:241681123-241683667	K562	blood:	n/a	n/a
4	POLR2A	chr1:241681074-241683713	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:241654504..241656882-chr1:241679445..241682289,2	K562	blood:
2	chr1:241676840..241679427-chr1:241681305..241683481,5	MCF-7	breast:
3	chr1:241680902..241684541-chr1:242009942..242012706,4	K562	blood:

Variant related genes	Relation type
FH	TF binding region
ENSG00000091483	Chromatin interaction
ENSG00000174371	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10926507	0.89[EUR][1000 genomes]
rs1335898	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1414493	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2153694	0.87[EUR][1000 genomes]
rs2992644	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2994982	0.87[EUR][1000 genomes]
rs2994985	0.87[EUR][1000 genomes]
rs2994987	0.87[EUR][1000 genomes]
rs2994989	0.87[EUR][1000 genomes]
rs4310432	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4659607	0.87[EUR][1000 genomes]
rs6679290	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv949442	chr1:241432051-241730054	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv873371	chr1:241667244-241747838	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241659000-241682000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:241661200-241681400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:241667400-241681800	Weak transcription	Fetal Brain Male	brain
4	chr1:241667600-241681800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:241667800-241682000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:241668000-241682000	Weak transcription	Pancreas	Pancrea
7	chr1:241668000-241682200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:241668000-241682200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:241668000-241682200	Weak transcription	Esophagus	oesophagus
10	chr1:241671800-241682000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:241672000-241681400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:241672000-241682000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:241672200-241681800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:241673200-241682200	Weak transcription	Spleen	Spleen
15	chr1:241674800-241681400	Weak transcription	Thymus	Thymus
16	chr1:241674800-241681800	Weak transcription	Small Intestine	intestine
17	chr1:241674800-241682000	Weak transcription	Colonic Mucosa	Colon
18	chr1:241675200-241681400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:241675400-241681800	Weak transcription	Ovary	ovary
20	chr1:241675600-241681400	Weak transcription	HSMMtube	muscle
21	chr1:241675600-241681800	Weak transcription	Brain Germinal Matrix	brain
22	chr1:241675800-241681400	Weak transcription	Brain Angular Gyrus	brain
23	chr1:241675800-241681800	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr1:241675800-241681800	Weak transcription	Left Ventricle	heart
25	chr1:241675800-241681800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:241675800-241682000	Weak transcription	Aorta	Aorta
27	chr1:241675800-241682200	Weak transcription	Lung	lung
28	chr1:241676000-241681400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:241676000-241681400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:241676000-241681400	Weak transcription	Right Ventricle	heart
31	chr1:241676000-241681800	Weak transcription	Psoas Muscle	Psoas
32	chr1:241676000-241682000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:241676000-241682200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:241676400-241681800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:241676400-241681800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:241676600-241682000	Weak transcription	Placenta	Placenta
37	chr1:241677000-241681400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:241677000-241681400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr1:241677000-241681800	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr1:241677000-241681800	Weak transcription	HSMM	muscle
41	chr1:241678800-241681600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:241678800-241681600	Weak transcription	Right Atrium	heart
43	chr1:241678800-241682000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:241679200-241681400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr1:241679800-241681800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr1:241680000-241681400	Weak transcription	Fetal Intestine Large	intestine
47	chr1:241680000-241681600	Weak transcription	Fetal Muscle Leg	muscle
48	chr1:241680000-241681800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:241680000-241681800	Weak transcription	Fetal Muscle Trunk	muscle
50	chr1:241680000-241682000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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