Variant report

Variant	rs1216799
Chromosome Location	chr1:113671013-113671014
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:113670754-113671275	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr1:113670566-113673475	K562	blood:	n/a	n/a
3	FOS	chr1:113670829-113671151	HUVEC	blood vessel:	n/a	chr1:113670972-113670983

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113666553..113668517-chr1:113670705..113672359,2	K562	blood:

Variant related genes	Relation type
RLIMP2	TF binding region

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

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11102593	1.00[AMR][1000 genomes]
rs11102594	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1216771	0.81[AFR][1000 genomes]
rs1216777	1.00[AMR][1000 genomes]
rs1216794	0.96[AFR][1000 genomes]
rs1216795	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs1216806	0.96[AFR][1000 genomes]
rs1216809	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs1216811	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs1216891	1.00[AMR][1000 genomes]
rs1216902	1.00[AMR][1000 genomes]
rs1632505	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030860	1.00[AMR][1000 genomes]
rs1728231	1.00[AMR][1000 genomes]
rs1766861	0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs4839289	1.00[AFR][1000 genomes]
rs6674506	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7555465	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs946217	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
8	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
9	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
10	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

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113633600-113672600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:113633800-113672600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:113634200-113671400	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:113634200-113673000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:113634400-113672600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr1:113634600-113671200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:113634600-113671600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr1:113634600-113673000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:113636000-113671200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:113636000-113671400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:113636000-113671400	Strong transcription	Fetal Thymus	thymus
12	chr1:113636000-113671600	Strong transcription	Duodenum Mucosa	Duodenum
13	chr1:113646400-113672600	Strong transcription	Placenta	Placenta
14	chr1:113651000-113671200	Strong transcription	Fetal Muscle Trunk	muscle
15	chr1:113653600-113673000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:113656600-113672400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:113656800-113671600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:113657000-113671200	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr1:113657000-113673000	Strong transcription	Primary T cells from cord blood	blood
20	chr1:113657000-113673400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:113662600-113675000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:113663400-113683400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:113663600-113671400	Strong transcription	HMEC	breast
24	chr1:113666200-113671600	Strong transcription	Fetal Brain Female	brain
25	chr1:113667000-113672000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:113667200-113671200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:113667200-113671400	Strong transcription	HSMM	muscle
28	chr1:113667200-113675000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:113667200-113675200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:113667200-113675800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:113667200-113678400	Weak transcription	Pancreas	Pancrea
32	chr1:113667200-113682400	Weak transcription	Fetal Brain Male	brain
33	chr1:113667200-113683400	Weak transcription	Esophagus	oesophagus
34	chr1:113667200-113683400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:113667200-113683400	Weak transcription	A549	lung
36	chr1:113667400-113679000	Weak transcription	Colon Smooth Muscle	Colon
37	chr1:113667400-113685200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:113667600-113683600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:113667800-113671600	Weak transcription	Fetal Stomach	stomach
40	chr1:113667800-113672400	Weak transcription	Fetal Intestine Small	intestine
41	chr1:113667800-113683400	Weak transcription	Gastric	stomach
42	chr1:113667800-113683600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr1:113668000-113672400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:113668000-113674800	Weak transcription	Aorta	Aorta
45	chr1:113668200-113683200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:113668200-113683600	Weak transcription	Small Intestine	intestine
47	chr1:113668400-113672600	Weak transcription	Colonic Mucosa	Colon
48	chr1:113668400-113675000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:113668400-113675000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr1:113668400-113675000	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links