Variant report

Variant	rs16858733
Chromosome Location	chr1:161697977-161697978
allele	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	chr1:161591405..161593904-chr1:161697560..161699954,2	K562	blood:
2	chr1:161696233..161698594-chr1:161718488..161721013,2	MCF-7	breast:
3	chr1:161696482..161699035-chr1:161718061..161722028,6	K562	blood:
4	chr1:161657417..161659539-chr1:161696325..161698709,3	K562	blood:
5	chr1:161648385..161650314-chr1:161696093..161698220,2	K562	blood:
6	chr1:161696672..161698764-chr1:161719597..161721628,3	K562	blood:
7	chr1:161654373..161658306-chr1:161696464..161699587,3	MCF-7	breast:
8	chr1:161694367..161698874-chr1:161718174..161721030,6	MCF-7	breast:
9	chr1:161651291..161653505-chr1:161696476..161699114,3	K562	blood:
10	chr1:161697451..161700405-chr1:161734526..161737492,2	K562	blood:
11	chr1:161695918..161698329-chr1:161735226..161737077,2	MCF-7	breast:
12	chr1:161683127..161685809-chr1:161696033..161698160,3	MCF-7	breast:
13	chr1:161535342..161537175-chr1:161695826..161698506,2	MCF-7	breast:
14	chr1:161696821..161698460-chr1:161718041..161719561,2	K562	blood:
15	chr1:161640986..161643411-chr1:161696404..161699095,2	MCF-7	breast:
16	chr1:161645664..161648632-chr1:161696817..161700044,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000226889	Chromatin interaction
ENSG00000213075	Chromatin interaction
ENSG00000081721	Chromatin interaction
ENSG00000118217	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10494356	0.89[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs10799934	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10917746	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs10917753	0.84[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs10917754	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs10917809	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11586479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12048671	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs12567036	0.84[ASN][1000 genomes]
rs16858529	0.89[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs2050887	0.89[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs4468140	0.89[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs6427619	0.80[CHB][hapmap]
rs6427620	0.82[ASN][1000 genomes]
rs6427623	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6697814	0.81[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs6699725	0.89[CEU][hapmap]
rs67476681	0.84[ASN][1000 genomes]
rs72704099	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7522783	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7525788	0.80[CHB][hapmap]
rs7549967	0.90[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs905592	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv516773	chr1:161691433-161702763	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	n/a
6	nsv464195	chr1:161693003-161702792	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a
7	nsv548076	chr1:161693003-161702792	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a
8	esv3343743	chr1:161695553-161698101	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161695400-161698000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
2	chr1:161695400-161698200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr1:161695800-161698000	Active TSS	NHLF	lung
4	chr1:161696000-161698000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:161696200-161698200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:161696400-161698200	Active TSS	H9 Cell Line	embryonic stem cell
7	chr1:161697000-161698000	Flanking Active TSS	NH-A	brain
8	chr1:161697400-161698000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr1:161697400-161698000	Flanking Active TSS	GM12878-XiMat	blood
10	chr1:161697400-161698000	Flanking Active TSS	NHEK	skin
11	chr1:161697600-161698000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
12	chr1:161697600-161698000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
13	chr1:161697600-161698000	Enhancers	Primary B cells from cord blood	blood
14	chr1:161697600-161698000	Enhancers	Primary hematopoietic stem cells	blood
15	chr1:161697600-161698000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:161697600-161698000	Bivalent Enhancer	Fetal Thymus	thymus
17	chr1:161697600-161698000	Bivalent Enhancer	Thymus	Thymus
18	chr1:161697600-161698000	Active TSS	HMEC	breast
19	chr1:161697600-161698000	Enhancers	HSMM	muscle
20	chr1:161697600-161698000	Flanking Active TSS	K562	blood
21	chr1:161697600-161698200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
22	chr1:161697600-161698400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:161697600-161698400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:161697600-161698400	Weak transcription	Right Ventricle	heart
25	chr1:161697600-161698600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:161697600-161699600	Weak transcription	Hela-S3	cervix
27	chr1:161697600-161700200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:161697600-161700200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:161697600-161700200	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr1:161697600-161700800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:161697600-161700800	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr1:161697600-161700800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:161697800-161698000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr1:161697800-161698000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
35	chr1:161697800-161698000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:161697800-161698000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:161697800-161698000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:161697800-161698000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:161697800-161698000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:161697800-161698000	Enhancers	Muscle Satellite Cultured Cells	--
41	chr1:161697800-161698000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:161697800-161698000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:161697800-161698000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:161697800-161698000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr1:161697800-161698000	Enhancers	A549	lung
46	chr1:161697800-161698000	Bivalent Enhancer	HepG2	liver
47	chr1:161697800-161698000	Enhancers	NHDF-Ad	bronchial
48	chr1:161697800-161698000	Enhancers	Osteobl	bone
49	chr1:161697800-161698200	Enhancers	Fetal Brain Male	brain
50	chr1:161697800-161698400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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