Variant report

Variant	rs2002402
Chromosome Location	chr1:113424101-113424102
allele	A/C/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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113423306..113424369-chr1:113584838..113585867,15	MCF-7	breast:
2	chr1:113415161..113418488-chr1:113420570..113424322,4	K562	blood:
3	chr1:113423272..113424581-chr1:113497804..113499381,4	K562	blood:
4	chr1:113422315..113424969-chr1:113580165..113583110,2	K562	blood:
5	chr1:113421698..113424854-chr1:113496536..113501677,6	K562	blood:
6	chr1:113421698..113424521-chr1:113497162..113501677,6	K562	blood:
7	chr1:113423348..113424191-chr1:113615233..113616019,3	MCF-7	breast:
8	chr1:113423347..113424253-chr1:113498007..113499021,4	MCF-7	breast:
9	chr1:113392230..113394904-chr1:113422287..113425247,2	MCF-7	breast:
10	chr1:113422181..113424521-chr1:113435432..113438293,2	K562	blood:
11	chr1:113423539..113425457-chr1:113613953..113617483,4	K562	blood:
12	chr1:113423643..113425440-chr1:113613953..113616307,2	K562	blood:
13	chr1:113421587..113424736-chr1:113583992..113587746,3	K562	blood:
14	chr1:113423151..113424795-chr1:113615741..113617336,2	MCF-7	breast:
15	chr1:113423270..113424538-chr1:113584948..113585944,13	K562	blood:
16	chr1:113422357..113424436-chr1:113583945..113586627,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000215866	Chromatin interaction
ENSG00000224167	Chromatin interaction
ENSG00000198799	Chromatin interaction
ENSG00000226419	Chromatin interaction
ENSG00000155380	Chromatin interaction
ENSG00000238198	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10399593	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10776763	0.84[EUR][1000 genomes]
rs10857979	0.94[ASN][1000 genomes]
rs10857981	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10857982	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10857983	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11102559	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11102562	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11102565	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11102568	0.84[EUR][1000 genomes]
rs12025191	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12028967	0.86[EUR][1000 genomes]
rs12037621	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12043035	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1216538	0.89[ASN][1000 genomes]
rs1539625	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2360009	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2996295	0.94[ASN][1000 genomes]
rs4301628	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4839273	0.82[EUR][1000 genomes]
rs57549167	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61819971	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61819997	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6670866	0.89[ASN][1000 genomes]
rs6682142	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv818378	chr1:113263711-113434818	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv1008434	chr1:113288282-113447426	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
11	nsv1004102	chr1:113295805-113551210	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
12	esv3399982	chr1:113358580-113542255	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
13	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
14	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
15	esv3362439	chr1:113376621-113450321	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113415000-113424600	Weak transcription	Right Atrium	heart
2	chr1:113416000-113424600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:113417000-113424400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:113421200-113424400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:113421200-113424400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:113421200-113424600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:113421400-113424400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:113421400-113424600	Weak transcription	Fetal Brain Female	brain
9	chr1:113421400-113424800	Weak transcription	Brain Angular Gyrus	brain
10	chr1:113421400-113435200	Weak transcription	Fetal Heart	heart
11	chr1:113421600-113424600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:113422000-113425800	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr1:113422600-113424400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:113423200-113424600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:113423200-113424600	Enhancers	Stomach Mucosa	stomach
16	chr1:113423400-113425200	Enhancers	Brain Substantia Nigra	brain
17	chr1:113423400-113425400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:113423400-113425400	Enhancers	Brain Hippocampus Middle	brain
19	chr1:113423400-113425600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:113423400-113425600	Enhancers	NHEK	skin
21	chr1:113423400-113425800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:113423600-113424600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:113423600-113424800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:113423600-113425200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:113423600-113425400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:113423600-113425400	Enhancers	HMEC	breast
27	chr1:113423600-113425400	Enhancers	K562	blood
28	chr1:113423600-113425600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:113423600-113425600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:113423600-113425800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:113423600-113425800	Enhancers	HSMM	muscle
32	chr1:113423600-113426000	Enhancers	Fetal Muscle Leg	muscle
33	chr1:113423600-113426200	Enhancers	Placenta	Placenta
34	chr1:113423800-113424200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:113423800-113424200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
36	chr1:113423800-113424200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:113423800-113424400	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr1:113423800-113424600	Weak transcription	Esophagus	oesophagus
39	chr1:113423800-113424600	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr1:113423800-113425200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:113423800-113425600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:113423800-113425800	Enhancers	Muscle Satellite Cultured Cells	--
43	chr1:113423800-113425800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:113423800-113425800	Enhancers	Adipose Nuclei	Adipose
45	chr1:113423800-113425800	Enhancers	Duodenum Mucosa	Duodenum
46	chr1:113423800-113426600	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr1:113424000-113424600	Enhancers	Osteobl	bone
48	chr1:113424000-113425600	Enhancers	Colonic Mucosa	Colon

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