Variant report

Variant	rs13025827
Chromosome Location	chr2:74337353-74337354
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:74335555..74337935-chr2:74348747..74350804,2	MCF-7	breast:
2	chr2:74335291..74341165-chr2:74346061..74348984,7	K562	blood:
3	chr2:74336985..74342809-chr2:74343895..74348590,10	MCF-7	breast:
4	chr2:74207099..74209137-chr2:74336774..74339550,2	MCF-7	breast:
5	chr2:74215681..74218530-chr2:74336371..74337878,2	MCF-7	breast:
6	chr2:74303308..74305107-chr2:74335863..74338424,2	K562	blood:
7	chr2:74331300..74332894-chr2:74335535..74338121,2	MCF-7	breast:
8	chr2:74335713..74338068-chr2:74339184..74340724,2	MCF-7	breast:
9	chr2:74336308..74342547-chr2:74345865..74348984,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000237883	Chromatin interaction
ENSG00000257800	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1026150	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs1095969	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1095970	0.91[ASN][1000 genomes]
rs12465641	0.86[JPT][hapmap]
rs12996870	0.90[ASN][1000 genomes]
rs1667615	0.86[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.91[ASN][1000 genomes]
rs1667616	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1667622	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1723283	0.90[ASN][1000 genomes]
rs1723284	0.90[ASN][1000 genomes]
rs1723290	0.90[ASN][1000 genomes]
rs2122290	0.86[JPT][hapmap]
rs2280642	0.85[JPT][hapmap]
rs2421753	0.90[ASN][1000 genomes]
rs3099822	0.87[ASN][1000 genomes]
rs3099823	0.87[ASN][1000 genomes]
rs3108161	0.89[ASN][1000 genomes]
rs3108162	0.87[ASN][1000 genomes]
rs4429500	0.82[JPT][hapmap]
rs4452177	0.84[JPT][hapmap]
rs6707619	0.82[JPT][hapmap]
rs6758220	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs702463	0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs702464	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs828841	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs828843	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs828845	0.87[ASN][1000 genomes]
rs828846	0.87[ASN][1000 genomes]
rs828847	0.83[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.87[ASN][1000 genomes]
rs828848	0.87[ASN][1000 genomes]
rs828850	0.87[ASN][1000 genomes]
rs828864	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs828865	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs828867	0.90[JPT][hapmap]
rs828897	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs828898	0.89[ASN][1000 genomes]
rs828901	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874284	chr2:74283728-74348797	Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv874285	chr2:74283728-74355244	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv874286	chr2:74323500-74436721	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74322200-74346600	Weak transcription	Hela-S3	cervix
2	chr2:74328400-74339000	Weak transcription	K562	blood
3	chr2:74328600-74339400	Weak transcription	Stomach Mucosa	stomach
4	chr2:74329600-74347000	Weak transcription	HSMMtube	muscle
5	chr2:74330200-74347000	Weak transcription	Aorta	Aorta
6	chr2:74330400-74338000	Weak transcription	Left Ventricle	heart
7	chr2:74330400-74346800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr2:74330600-74341000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:74330600-74341200	Weak transcription	Spleen	Spleen
10	chr2:74330600-74346600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:74330600-74347000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:74330600-74347000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:74330600-74347000	Weak transcription	Pancreas	Pancrea
14	chr2:74330800-74346800	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:74330800-74347000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr2:74331000-74338800	Weak transcription	Brain Substantia Nigra	brain
17	chr2:74331000-74340400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:74331200-74338800	Weak transcription	Primary B cells from cord blood	blood
19	chr2:74331200-74347200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:74332000-74342000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:74332000-74346400	Weak transcription	Dnd41	blood
22	chr2:74332000-74346800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:74332400-74338200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:74332600-74339600	Weak transcription	Fetal Intestine Large	intestine
25	chr2:74332600-74346400	Weak transcription	GM12878-XiMat	blood
26	chr2:74332600-74347000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr2:74332600-74347000	Weak transcription	Esophagus	oesophagus
28	chr2:74332800-74346800	Weak transcription	NHEK	skin
29	chr2:74333000-74346800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:74333200-74337600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:74333200-74346800	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr2:74333200-74347000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:74333400-74338600	Weak transcription	Fetal Brain Female	brain
34	chr2:74333600-74338800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr2:74333600-74339000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:74333600-74346600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr2:74333800-74338400	Weak transcription	Lung	lung
38	chr2:74333800-74338800	Weak transcription	Fetal Stomach	stomach
39	chr2:74334400-74338800	Weak transcription	Gastric	stomach
40	chr2:74334600-74340000	Weak transcription	Fetal Thymus	thymus
41	chr2:74334800-74337600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:74335000-74338400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr2:74335600-74346800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:74336000-74347000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:74336200-74346600	Weak transcription	Primary T cells from cord blood	blood
46	chr2:74336200-74346600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr2:74336600-74338200	Weak transcription	Brain Germinal Matrix	brain

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