Variant report

Variant	rs10904955
Chromosome Location	chr10:5648966-5648967
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:5648567..5652209-chr10:5653862..5656338,4	MCF-7	breast:
2	chr10:5647810..5650378-chr10:5650517..5654278,5	MCF-7	breast:
3	chr10:5529023..5530899-chr10:5646975..5649867,2	MCF-7	breast:
4	chr10:5529293..5532175-chr10:5647723..5650596,3	MCF-7	breast:
5	chr10:5642990..5644643-chr10:5647471..5649799,2	K562	blood:
6	chr10:5486648..5491055-chr10:5645215..5653179,9	MCF-7	breast:
7	chr10:5483526..5484570-chr10:5648597..5649650,4	MCF-7	breast:
8	chr10:5648373..5651329-chr10:5728348..5730813,2	K562	blood:
9	chr10:5589034..5590699-chr10:5646988..5649600,2	MCF-7	breast:
10	chr10:5533616..5541618-chr10:5644676..5651501,11	MCF-7	breast:
11	chr10:5647085..5649408-chr10:5659482..5661422,2	MCF-7	breast:
12	chr10:5638529..5640411-chr10:5647235..5649668,2	MCF-7	breast:
13	chr10:5640782..5643006-chr10:5647481..5649125,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000231483	Chromatin interaction
ENSG00000178372	Chromatin interaction
ENSG00000228951	Chromatin interaction
ENSG00000173848	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs17138235	0.95[AFR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4747325	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4748280	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4748281	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4748295	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4748301	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4748304	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6602232	0.82[EUR][1000 genomes]
rs7896762	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7907173	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7919652	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
3	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
4	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
5	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
6	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
7	esv2758209	chr10:5637111-5804780	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1036798	chr10:5637870-5652754	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1040932	chr10:5637870-5665774	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv466718	chr10:5639907-5657527	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv549890	chr10:5639907-5657527	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv2753567	chr10:5641348-5652237	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv894806	chr10:5643511-5670275	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1054888	chr10:5645033-5694612	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv466719	chr10:5645895-5662915	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv549891	chr10:5645895-5662915	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	nsv519582	chr10:5646103-5720067	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
18	nsv894807	chr10:5647942-5691135	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5634800-5651200	Weak transcription	Pancreas	Pancrea
2	chr10:5639800-5650200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr10:5639800-5651600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr10:5642600-5651000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr10:5644200-5650600	Weak transcription	Liver	Liver
6	chr10:5645000-5651800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr10:5645600-5650400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:5646000-5650200	Weak transcription	HMEC	breast
9	chr10:5647000-5649200	Enhancers	Fetal Muscle Leg	muscle
10	chr10:5648000-5649000	Enhancers	NHEK	skin
11	chr10:5648200-5650000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr10:5648200-5650600	Weak transcription	Fetal Intestine Small	intestine
13	chr10:5648400-5649000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr10:5648400-5649000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr10:5648400-5649000	Enhancers	Esophagus	oesophagus
16	chr10:5648400-5649000	Enhancers	Left Ventricle	heart
17	chr10:5648400-5650600	Weak transcription	Fetal Intestine Large	intestine
18	chr10:5648600-5649000	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr10:5648600-5649200	Enhancers	Primary hematopoietic stem cells	blood
20	chr10:5648600-5649200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr10:5648600-5651000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr10:5648600-5651000	Weak transcription	A549	lung
23	chr10:5648600-5651200	Weak transcription	Fetal Thymus	thymus
24	chr10:5648600-5652000	Weak transcription	Lung	lung
25	chr10:5648800-5649000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
26	chr10:5648800-5649000	Enhancers	Stomach Mucosa	stomach
27	chr10:5648800-5649200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr10:5648800-5651000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links