Variant report

Variant	rs1999996
Chromosome Location	chr1:184532090-184532091
allele	A/C/G/T
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	CTCF	chr1:184531982-184533197	SK-N-SH	brain:	n/a	n/a
2	RAD21	chr1:184531400-184533136	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr1:184532060-184532210	GM06990	blood:	n/a	n/a
4	SMC3	chr1:184532019-184533113	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:184531076..184532675-chr1:184595685..184597325,2	MCF-7	breast:
2	chr1:184508816..184510741-chr1:184531870..184534082,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232036	TF binding region
ENSG00000116667	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10797974	0.81[AMR][1000 genomes]
rs10797979	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10911613	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10911614	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10911618	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12134281	0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1339573	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1569843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1569844	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1572767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1856562	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1985703	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2890014	0.87[AMR][1000 genomes]
rs4651218	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4651221	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4651224	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6424958	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6424959	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6424960	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6667692	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6674023	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6674115	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6696816	0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs749214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs946547	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer 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	10 gene(s)	inside rSNPs	diseases
3	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer 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	69 gene(s)	inside rSNPs	diseases
4	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1999996	C1orf21	cis	Nerve Tibial	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184512200-184543600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:184514400-184543800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr1:184520800-184542000	Weak transcription	Ovary	ovary
4	chr1:184521000-184535800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:184521000-184547400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:184525000-184546000	Weak transcription	Brain Angular Gyrus	brain
7	chr1:184525200-184535200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:184525400-184535200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:184525600-184536000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:184525600-184544000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:184525600-184545600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:184525800-184535200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:184526600-184535600	Weak transcription	Left Ventricle	heart
14	chr1:184528600-184535400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:184528600-184536400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:184529200-184535400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:184529800-184532600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:184530200-184532200	Enhancers	Stomach Smooth Muscle	stomach
19	chr1:184530200-184532600	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr1:184530200-184532800	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr1:184530200-184533000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:184530600-184532200	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr1:184530600-184532400	Enhancers	Stomach Mucosa	stomach
24	chr1:184530600-184532400	Enhancers	HSMM	muscle
25	chr1:184530600-184535200	Weak transcription	Pancreas	Pancrea
26	chr1:184530800-184532400	Enhancers	Rectal Smooth Muscle	rectum
27	chr1:184530800-184533200	Enhancers	Colon Smooth Muscle	Colon
28	chr1:184531000-184532400	Enhancers	HSMMtube	muscle
29	chr1:184531000-184532600	Enhancers	Adipose Nuclei	Adipose
30	chr1:184531000-184536000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:184531000-184543800	Weak transcription	Esophagus	oesophagus
32	chr1:184531200-184532400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:184531200-184532400	Enhancers	NHDF-Ad	bronchial
34	chr1:184531200-184532400	Enhancers	NHLF	lung
35	chr1:184531200-184532600	Enhancers	Fetal Heart	heart
36	chr1:184531200-184532800	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr1:184531200-184533000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:184531400-184532200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:184531400-184532200	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr1:184531400-184532200	Enhancers	Brain Anterior Caudate	brain
41	chr1:184531400-184532200	Enhancers	Fetal Lung	lung
42	chr1:184531400-184532400	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr1:184531400-184532600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:184531400-184532800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:184531400-184533000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr1:184531400-184533200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:184531400-184543200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:184531600-184532200	Enhancers	Fetal Stomach	stomach
49	chr1:184531600-184532400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:184531600-184536000	Weak transcription	HMEC	breast

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