Variant report

Variant	rs4242799
Chromosome Location	chr10:5598603-5598604
allele	A/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:1)
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	chr10:5595300..5599425-chr10:5700368..5703903,3	MCF-7	breast:
2	chr10:5508799..5510364-chr10:5598163..5599717,2	K562	blood:
3	chr10:5583637..5601494-chr10:5650599..5672411,88	MCF-7	breast:
4	chr10:5597404..5599365-chr10:5605126..5607018,2	K562	blood:
5	chr10:5579554..5581874-chr10:5597912..5600159,2	K562	blood:
6	chr10:5594566..5598758-chr10:5599072..5603541,5	K562	blood:
7	chr10:5596247..5598987-chr10:5697785..5700131,2	MCF-7	breast:
8	chr10:5544425..5547026-chr10:5598488..5600263,2	MCF-7	breast:
9	chr10:5596817..5599618-chr10:5614255..5615929,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CALML5-7	chr10:5598499-5598689	l_246_chr10:5596689-5598689_testes

No data

Variant related genes	Relation type
ENSG00000228685	Chromatin interaction
ENSG00000231483	Chromatin interaction
ENSG00000228951	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11253225	0.86[ASN][1000 genomes]
rs11253226	0.89[ASN][1000 genomes]
rs11253227	0.89[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs35850659	0.84[AMR][1000 genomes]
rs7079395	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs9423443	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv932104	chr10:5203626-5641023	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv549886	chr10:5205437-5632060	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv1054865	chr10:5225305-5638119	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv831774	chr10:5463556-5657421	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv894798	chr10:5503610-5670275	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv1051283	chr10:5505474-5619941	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1049523	chr10:5542109-5619941	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv523491	chr10:5542109-5720067	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv1052002	chr10:5544571-5619941	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv1038479	chr10:5545773-5619941	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	esv2757364	chr10:5557024-5720512	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
13	esv2759729	chr10:5557024-5804780	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
14	nsv894800	chr10:5572893-5621628	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
15	nsv470915	chr10:5591025-5602880	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv1044746	chr10:5595343-5619941	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5588400-5608200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr10:5590200-5599400	Enhancers	Fetal Intestine Small	intestine
3	chr10:5590200-5599800	Enhancers	Fetal Intestine Large	intestine
4	chr10:5591400-5605400	Weak transcription	Right Atrium	heart
5	chr10:5593400-5601600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr10:5593600-5601000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr10:5594600-5601400	Weak transcription	HSMMtube	muscle
8	chr10:5595200-5599000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr10:5595200-5604800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr10:5595600-5606200	Weak transcription	Spleen	Spleen
11	chr10:5595800-5599400	Enhancers	Rectal Smooth Muscle	rectum
12	chr10:5596400-5599600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr10:5596600-5599400	Weak transcription	Placenta	Placenta
14	chr10:5596600-5600200	Weak transcription	NH-A	brain
15	chr10:5596600-5601400	Weak transcription	HSMM	muscle
16	chr10:5596600-5601400	Weak transcription	NHEK	skin
17	chr10:5596600-5605400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr10:5596800-5600800	Weak transcription	NHDF-Ad	bronchial
19	chr10:5596800-5601000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr10:5596800-5601200	Weak transcription	A549	lung
21	chr10:5596800-5601400	Weak transcription	Fetal Thymus	thymus
22	chr10:5596800-5601800	Weak transcription	Fetal Brain Female	brain
23	chr10:5596800-5601800	Weak transcription	HMEC	breast
24	chr10:5596800-5603600	Enhancers	HepG2	liver
25	chr10:5597000-5600000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr10:5597000-5600200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr10:5597000-5600600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr10:5597000-5600800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr10:5597000-5601400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr10:5597000-5601600	Weak transcription	Primary T cells from cord blood	blood
31	chr10:5597000-5603400	Enhancers	Stomach Smooth Muscle	stomach
32	chr10:5597200-5599000	Enhancers	Aorta	Aorta
33	chr10:5597200-5600600	Weak transcription	Fetal Muscle Leg	muscle
34	chr10:5597200-5600800	Weak transcription	Osteobl	bone
35	chr10:5597200-5601200	Weak transcription	HUVEC	blood vessel
36	chr10:5597200-5601800	Weak transcription	Fetal Lung	lung
37	chr10:5597400-5601600	Weak transcription	Hela-S3	cervix
38	chr10:5597400-5602200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr10:5597600-5599600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr10:5597600-5599800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr10:5597600-5601600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr10:5597600-5606000	Weak transcription	Gastric	stomach
43	chr10:5597800-5605400	Weak transcription	Esophagus	oesophagus
44	chr10:5598000-5600200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr10:5598400-5598800	Enhancers	Fetal Muscle Trunk	muscle
46	chr10:5598400-5599800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr10:5598600-5598800	Enhancers	Brain Anterior Caudate	brain
48	chr10:5598600-5599000	Enhancers	K562	blood
49	chr10:5598600-5599200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr10:5598600-5599400	Enhancers	Colon Smooth Muscle	Colon

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