Variant report

Variant	rs13418799
Chromosome Location	chr2:152146287-152146288
allele	A/G
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:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:152116868..152120610-chr2:152144685..152147660,4	MCF-7	breast:
2	chr2:152145011..152148288-chr2:152265460..152267609,4	MCF-7	breast:
3	chr2:152117973..152120026-chr2:152143620..152147532,3	K562	blood:
4	chr2:152144662..152146339-chr2:152277949..152280941,2	MCF-7	breast:
5	chr2:152145849..152146532-chr2:152266419..152266964,2	MCF-7	breast:
6	chr2:152144813..152149803-chr2:152261382..152268379,11	K562	blood:
7	chr2:152146182..152146803-chr2:152266084..152266913,2	MCF-7	breast:
8	chr2:152115426..152120009-chr2:152142898..152146726,5	K562	blood:
9	chr2:152117804..152120182-chr2:152144785..152147621,2	MCF-7	breast:
10	chr2:152144798..152147073-chr2:152265350..152268359,5	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RBM43-3	chr2:152146107-152146377	NONHSAT074950

No data

Variant related genes	Relation type
ENSG00000080345	Chromatin interaction
ENSG00000184898	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10173695	1.00[AMR][1000 genomes]
rs10179626	1.00[AMR][1000 genomes]
rs10180428	1.00[AMR][1000 genomes]
rs10190464	1.00[AMR][1000 genomes]
rs10191465	1.00[AMR][1000 genomes]
rs10193304	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10195365	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10201647	1.00[AMR][1000 genomes]
rs10202368	1.00[AMR][1000 genomes]
rs10203338	1.00[AMR][1000 genomes]
rs10205770	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10205976	1.00[AMR][1000 genomes]
rs10206584	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10210009	1.00[AMR][1000 genomes]
rs12328054	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12328381	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12328560	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13383657	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13385932	1.00[AMR][1000 genomes]
rs13387765	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13389056	1.00[AMR][1000 genomes]
rs13389461	1.00[AMR][1000 genomes]
rs13390792	1.00[AMR][1000 genomes]
rs13394505	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13395395	1.00[AMR][1000 genomes]
rs13395749	1.00[AMR][1000 genomes]
rs13399299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13404713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13408667	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13408684	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13411396	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13412493	1.00[AMR][1000 genomes]
rs13412781	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13417120	1.00[AMR][1000 genomes]
rs13418019	1.00[AMR][1000 genomes]
rs13420365	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13423692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13426840	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2303341	1.00[AMR][1000 genomes]
rs28445248	1.00[AMR][1000 genomes]
rs28493579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28529741	1.00[AMR][1000 genomes]
rs3771899	1.00[AMR][1000 genomes]
rs56801020	1.00[AMR][1000 genomes]
rs59089077	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59356545	1.00[AMR][1000 genomes]
rs6719796	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6724871	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6747290	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9989812	1.00[AFR][1000 genomes];1.00[AMR][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	esv3693426	chr2:151725792-152295862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv834417	chr2:151980473-152154950	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1012891	chr2:152019809-152306897	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1013484	chr2:152028515-152473913	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv535983	chr2:152028515-152473913	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1012139	chr2:152114637-152389516	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1011339	chr2:152114637-152392940	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv999748	chr2:152135514-152476396	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
9	esv1793984	chr2:152138749-152154163	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152144400-152146800	Active TSS	A549	lung
2	chr2:152144400-152147200	Active TSS	GM12878-XiMat	blood
3	chr2:152144800-152147000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:152144800-152147000	Active TSS	Rectal Smooth Muscle	rectum
5	chr2:152144800-152147000	Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr2:152144800-152147200	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr2:152145000-152147200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:152145200-152146600	Active TSS	NHLF	lung
9	chr2:152145200-152146800	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr2:152145200-152146800	Active TSS	Right Ventricle	heart
11	chr2:152145200-152147000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:152145200-152147000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:152145200-152147000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:152145200-152147000	Active TSS	Brain Cingulate Gyrus	brain
15	chr2:152145200-152147000	Active TSS	Brain Hippocampus Middle	brain
16	chr2:152145200-152147000	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr2:152145200-152147000	Active TSS	Brain Substantia Nigra	brain
18	chr2:152145200-152147000	Active TSS	Colon Smooth Muscle	Colon
19	chr2:152145200-152147000	Active TSS	Duodenum Mucosa	Duodenum
20	chr2:152145200-152147000	Active TSS	Psoas Muscle	Psoas
21	chr2:152145200-152147000	Active TSS	Right Atrium	heart
22	chr2:152145200-152147000	Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr2:152145200-152147000	Active TSS	Stomach Smooth Muscle	stomach
24	chr2:152145200-152147000	Active TSS	Hela-S3	cervix
25	chr2:152145200-152147000	Active TSS	HSMMtube	muscle
26	chr2:152145200-152147000	Active TSS	Osteobl	bone
27	chr2:152145200-152147200	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr2:152145200-152147200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:152145400-152146400	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr2:152145400-152146400	Active TSS	Spleen	Spleen
31	chr2:152145400-152146600	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr2:152145400-152146600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:152145400-152146600	Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr2:152145400-152146600	Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr2:152145400-152146600	Active TSS	HUVEC	blood vessel
36	chr2:152145400-152146800	Active TSS	Primary T cells from cord blood	blood
37	chr2:152145400-152146800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr2:152145400-152146800	Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr2:152145400-152146800	Active TSS	Adipose Nuclei	Adipose
40	chr2:152145400-152146800	Active TSS	Liver	Liver
41	chr2:152145400-152146800	Active TSS	Esophagus	oesophagus
42	chr2:152145400-152146800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr2:152145400-152146800	Active TSS	Fetal Lung	lung
44	chr2:152145400-152146800	Active TSS	Gastric	stomach
45	chr2:152145400-152146800	Active TSS	Sigmoid Colon	Sigmoid Colon
46	chr2:152145400-152146800	Active TSS	Small Intestine	intestine
47	chr2:152145400-152146800	Active TSS	Stomach Mucosa	stomach
48	chr2:152145400-152146800	Active TSS	Dnd41	blood
49	chr2:152145400-152146800	Active TSS	K562	blood
50	chr2:152145400-152147000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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