Variant report

Variant	rs56407824
Chromosome Location	chr2:101195413-101195414
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	chr2:101178362..101181759-chr2:101194007..101196018,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115539	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11123838	0.83[ASN][1000 genomes]
rs12151415	0.88[AMR][1000 genomes]
rs12469806	0.81[ASN][1000 genomes]
rs2946595	0.88[AMR][1000 genomes]
rs2970993	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34940694	0.84[AMR][1000 genomes]
rs35658386	0.84[ASN][1000 genomes]
rs56242838	0.82[ASN][1000 genomes]
rs57619803	0.86[ASN][1000 genomes]
rs59729787	0.87[AMR][1000 genomes]
rs60927663	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62152478	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6705682	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6728833	0.88[AMR][1000 genomes]
rs6728834	0.88[AMR][1000 genomes]
rs6731795	0.88[AMR][1000 genomes]
rs72966916	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7587860	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7594990	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv582531	chr2:100908508-101207639	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv916792	chr2:101021066-101525200	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers 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	28 gene(s)	inside rSNPs	diseases
5	nsv582532	chr2:101029002-101531943	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv834312	chr2:101044438-101238166	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:101180600-101197800	Weak transcription	Stomach Mucosa	stomach
2	chr2:101180800-101195600	Weak transcription	Fetal Heart	heart
3	chr2:101180800-101195800	Strong transcription	Fetal Stomach	stomach
4	chr2:101180800-101196800	Weak transcription	NHLF	lung
5	chr2:101180800-101197000	Weak transcription	Colonic Mucosa	Colon
6	chr2:101180800-101197200	Weak transcription	Small Intestine	intestine
7	chr2:101181000-101195800	Strong transcription	Fetal Muscle Trunk	muscle
8	chr2:101181400-101195800	Strong transcription	Fetal Muscle Leg	muscle
9	chr2:101181400-101196200	Weak transcription	Gastric	stomach
10	chr2:101181400-101196800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:101181600-101196600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:101181600-101197200	Weak transcription	Brain Angular Gyrus	brain
13	chr2:101182600-101195800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:101182600-101195800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:101182800-101195600	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr2:101183800-101204200	Weak transcription	Hela-S3	cervix
17	chr2:101184000-101197600	Weak transcription	NHEK	skin
18	chr2:101184200-101196400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:101184200-101197600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:101186400-101197000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:101187600-101196600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr2:101188400-101196400	Weak transcription	Psoas Muscle	Psoas
23	chr2:101188400-101197200	Weak transcription	Spleen	Spleen
24	chr2:101188600-101195600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr2:101188600-101195600	Weak transcription	A549	lung
26	chr2:101188600-101196600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr2:101188600-101196600	Weak transcription	Thymus	Thymus
28	chr2:101188600-101197000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr2:101188600-101197400	Weak transcription	HSMMtube	muscle
30	chr2:101188600-101204200	Weak transcription	K562	blood
31	chr2:101188800-101197000	Weak transcription	Brain Anterior Caudate	brain
32	chr2:101188800-101197200	Weak transcription	Osteobl	bone
33	chr2:101189200-101196800	Weak transcription	Brain Germinal Matrix	brain
34	chr2:101189800-101196600	Weak transcription	Fetal Thymus	thymus
35	chr2:101190400-101196400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:101191200-101197600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:101191400-101197000	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:101191600-101196400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr2:101191600-101196600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr2:101191600-101197800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr2:101192000-101197200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:101192200-101195600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr2:101192400-101195800	Weak transcription	Primary T cells from cord blood	blood
44	chr2:101192400-101197000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:101192400-101197200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr2:101192600-101197000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:101192600-101197000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr2:101192800-101195600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:101192800-101196200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:101192800-101197000	Weak transcription	Brain Substantia Nigra	brain

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