Variant report

Variant	rs13395559
Chromosome Location	chr2:180014446-180014447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179628215..179630011-chr2:180014131..180016832,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10172589	1.00[ASN][1000 genomes]
rs10173853	1.00[AMR][1000 genomes]
rs10176828	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10178559	1.00[AMR][1000 genomes]
rs10186707	1.00[AMR][1000 genomes]
rs10205588	1.00[AMR][1000 genomes]
rs10207754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10208882	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10209875	1.00[CHB][hapmap]
rs10221811	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12328593	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12329222	0.91[ASN][1000 genomes]
rs12611473	1.00[AMR][1000 genomes]
rs12612427	1.00[AMR][1000 genomes]
rs12613089	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs12616452	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12617364	1.00[AMR][1000 genomes]
rs12618724	0.85[ASN][1000 genomes]
rs12622434	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13382573	1.00[AMR][1000 genomes]
rs13383806	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13387502	0.85[ASN][1000 genomes]
rs13391187	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13394908	1.00[AMR][1000 genomes]
rs13408774	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13412820	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13417112	1.00[AMR][1000 genomes]
rs13422693	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13424092	1.00[CHB][hapmap]
rs13429191	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16866630	1.00[AMR][1000 genomes]
rs16866647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs28362046	0.90[ASN][1000 genomes]
rs28508327	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35041512	1.00[AMR][1000 genomes]
rs6734127	1.00[AMR][1000 genomes]
rs7578417	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7581898	1.00[AMR][1000 genomes]
rs7588135	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7601965	1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7608106	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9288024	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv3060	chr2:179990791-180035511	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179972800-180014600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:179973400-180030200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:179975800-180047600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:179977400-180049000	Weak transcription	HSMMtube	muscle
5	chr2:179978200-180014600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:179980000-180038800	Weak transcription	HMEC	breast
7	chr2:179980000-180056800	Weak transcription	HSMM	muscle
8	chr2:179981400-180016800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:179985000-180025600	Weak transcription	Fetal Intestine Small	intestine
10	chr2:179986600-180030400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:179991600-180043200	Weak transcription	Psoas Muscle	Psoas
12	chr2:179992200-180014600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:179995800-180016200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr2:179996200-180047600	Weak transcription	NH-A	brain
15	chr2:179998000-180060600	Weak transcription	Right Ventricle	heart
16	chr2:180000600-180016200	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr2:180000600-180016200	Strong transcription	Primary B cells from peripheral blood	blood
18	chr2:180001200-180016200	Strong transcription	HepG2	liver
19	chr2:180002400-180016400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:180002400-180030200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:180003200-180039800	Weak transcription	Brain Germinal Matrix	brain
22	chr2:180003800-180016200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:180004800-180019200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:180004800-180046000	Weak transcription	Spleen	Spleen
25	chr2:180005000-180028800	Weak transcription	Hela-S3	cervix
26	chr2:180005600-180014600	Weak transcription	Lung	lung
27	chr2:180005600-180040200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr2:180005600-180044400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:180005600-180044400	Weak transcription	Esophagus	oesophagus
30	chr2:180005800-180018200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:180005800-180030200	Weak transcription	Thymus	Thymus
32	chr2:180005800-180043200	Weak transcription	Fetal Brain Male	brain
33	chr2:180005800-180053600	Weak transcription	Primary T cells from cord blood	blood
34	chr2:180006000-180014600	Weak transcription	Fetal Stomach	stomach
35	chr2:180006000-180030600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr2:180006000-180044600	Weak transcription	Pancreas	Pancrea
37	chr2:180006200-180014600	Weak transcription	Gastric	stomach
38	chr2:180006200-180014800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:180006200-180016600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr2:180006200-180031400	Weak transcription	Brain Hippocampus Middle	brain
41	chr2:180006200-180031400	Weak transcription	Fetal Brain Female	brain
42	chr2:180006400-180030200	Weak transcription	Fetal Muscle Leg	muscle
43	chr2:180006600-180014600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr2:180006600-180042000	Weak transcription	Brain Substantia Nigra	brain
45	chr2:180006600-180051000	Weak transcription	HUVEC	blood vessel
46	chr2:180006800-180014600	Weak transcription	Ovary	ovary
47	chr2:180006800-180031600	Weak transcription	Brain Anterior Caudate	brain
48	chr2:180006800-180054600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr2:180007200-180028600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:180007400-180035200	Weak transcription	Colon Smooth Muscle	Colon

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