Variant report

Variant	rs1778027
Chromosome Location	chr1:113635468-113635469
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113634658..113637321-chr1:113637613..113639696,2	MCF-7	breast:
2	chr1:113633112..113636073-chr1:113643348..113646226,2	K562	blood:
3	chr1:113615241..113617330-chr1:113632908..113635884,2	MCF-7	breast:
4	chr1:113635215..113637983-chr1:114201241..114204129,2	K562	blood:
5	chr1:113629031..113632122-chr1:113632833..113640329,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198799	Chromatin interaction
ENSG00000238198	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11102579	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11102581	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11102582	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1216760	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1216762	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1216763	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1216766	0.80[ASN][1000 genomes]
rs1216768	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1216780	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1216781	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1216801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1216804	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12568813	0.90[EUR][1000 genomes]
rs12744009	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12758163	0.91[EUR][1000 genomes]
rs1419136	0.80[ASN][1000 genomes]
rs1619133	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1626085	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17030974	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1728230	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1728238	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1766862	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1766863	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1778015	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1778018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1778024	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1778025	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1778028	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2485964	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2798686	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2798687	0.80[ASN][1000 genomes]
rs2840294	0.89[EUR][1000 genomes]
rs2950632	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4025965	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72683488	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
5	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
6	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
7	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
8	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
9	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
10	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
11	nsv946146	chr1:113567302-113640814	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
13	nsv508537	chr1:113590343-113635803	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv437002	chr1:113592588-113658887	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113616800-113638600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:113617000-113636800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:113617000-113636800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:113617000-113638400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:113617000-113645800	Weak transcription	Aorta	Aorta
6	chr1:113617200-113635800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:113617200-113636400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:113617200-113636400	Weak transcription	HSMMtube	muscle
9	chr1:113617200-113636400	Weak transcription	NHDF-Ad	bronchial
10	chr1:113617200-113642600	Weak transcription	A549	lung
11	chr1:113617400-113638000	Weak transcription	NHLF	lung
12	chr1:113617800-113637200	Weak transcription	Psoas Muscle	Psoas
13	chr1:113617800-113637800	Weak transcription	Spleen	Spleen
14	chr1:113617800-113638000	Weak transcription	Gastric	stomach
15	chr1:113619600-113636600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr1:113621800-113635600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:113622000-113636000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr1:113622000-113636000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:113622000-113636000	Weak transcription	HMEC	breast
20	chr1:113622000-113636000	Weak transcription	Osteobl	bone
21	chr1:113622000-113636400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:113622000-113637200	Weak transcription	Colonic Mucosa	Colon
23	chr1:113622000-113637800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:113622000-113638400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:113622000-113638400	Weak transcription	Brain Germinal Matrix	brain
26	chr1:113622200-113636000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:113622200-113645600	Weak transcription	Right Ventricle	heart
28	chr1:113622200-113645800	Weak transcription	Lung	lung
29	chr1:113622800-113636400	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr1:113624000-113638400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:113624400-113637800	Weak transcription	Pancreas	Pancrea
32	chr1:113625200-113637200	Weak transcription	Thymus	Thymus
33	chr1:113625200-113638200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:113625800-113646000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:113626400-113637200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:113626400-113638200	Weak transcription	Esophagus	oesophagus
37	chr1:113628000-113636600	Weak transcription	HUVEC	blood vessel
38	chr1:113628200-113635800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:113628200-113637200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:113628400-113636000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:113628400-113636400	Weak transcription	Adipose Nuclei	Adipose
42	chr1:113628800-113636000	Weak transcription	Small Intestine	intestine
43	chr1:113629800-113637800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:113630000-113636400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:113630800-113636000	Weak transcription	Primary T cells from cord blood	blood
46	chr1:113630800-113636600	Weak transcription	Fetal Kidney	kidney
47	chr1:113630800-113638600	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr1:113631000-113638400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr1:113631600-113638000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:113631800-113638800	Weak transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links