Variant report

Variant	rs16862217
Chromosome Location	chr1:169452184-169452185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:169451944-169452257	MCF-7	breast:	n/a	n/a
2	POLR2A	chr1:169451934-169453706	K562	blood:	n/a	n/a
3	SPI1	chr1:169451840-169452204	HL-60	blood:	n/a	n/a
4	POLR2A	chr1:169451926-169456727	IMR90	lung:	n/a	n/a
5	MYC	chr1:169451807-169452418	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:169451858..169456935-chr1:169476541..169486862,15	MCF-7	breast:
2	chr1:169428536..169430863-chr1:169451257..169453654,2	K562	blood:
3	chr1:169337822..169339719-chr1:169451874..169454199,3	K562	blood:
4	chr1:169449894..169459462-chr1:169475885..169501963,75	MCF-7	breast:
5	chr1:169338121..169342264-chr1:169451874..169455112,4	K562	blood:
6	chr1:169437031..169439523-chr1:169451162..169453352,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000213062	TF binding region
ENSG00000234437	Chromatin interaction
ENSG00000117477	Chromatin interaction
ENSG00000198734	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10158131	0.82[CHB][hapmap]
rs1028180	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10753786	0.88[CHB][hapmap]
rs10919132	0.81[CHB][hapmap]
rs10919140	0.82[CHB][hapmap]
rs10919173	0.82[CHB][hapmap]
rs12040141	1.00[CEU][hapmap]
rs12121994	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12143193	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12145146	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs12145226	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12727318	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12729761	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12733001	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs12733037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12733626	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12744859	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12752953	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13306334	1.00[CEU][hapmap]
rs1517745	0.81[CHB][hapmap]
rs1533518	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1533519	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16862081	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs16862097	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16862133	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16862153	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16862176	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16862180	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs16862236	0.88[EUR][1000 genomes]
rs1883167	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2037249	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2066001	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2203743	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2271762	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2272801	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2300157	0.82[CHB][hapmap]
rs2300158	0.88[CHB][hapmap]
rs2420015	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs2420016	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs3213586	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs3213587	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs34057682	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34373126	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34599582	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34640648	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34858340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34989506	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35171152	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs35686518	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35918529	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3765229	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3766090	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs3766097	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3862937	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4140538	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs4140539	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs4551642	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4590731	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs57295069	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs58809384	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs66512221	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6672589	0.82[CHB][hapmap]
rs66937324	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs67795749	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72637232	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7551623	1.00[CEU][hapmap]
rs929133	0.88[CHB][hapmap]
rs9332623	1.00[CEU][hapmap]
rs9332624	1.00[CEU][hapmap]
rs9332628	1.00[CEU][hapmap]
rs9332647	1.00[CEU][hapmap]
rs9332658	1.00[CEU][hapmap]
rs9332678	1.00[CEU][hapmap]

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	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer 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	28 gene(s)	inside rSNPs	diseases
3	nsv1001454	chr1:169387381-169465274	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1005941	chr1:169410486-169456393	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169430000-169452600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:169430000-169452800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:169430000-169452800	Weak transcription	Brain Germinal Matrix	brain
4	chr1:169430000-169452800	Weak transcription	HMEC	breast
5	chr1:169430000-169452800	Weak transcription	NHDF-Ad	bronchial
6	chr1:169430000-169452800	Weak transcription	NHEK	skin
7	chr1:169430000-169453400	Weak transcription	Colonic Mucosa	Colon
8	chr1:169430000-169453800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:169430000-169454000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:169430000-169454400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:169430000-169454400	Weak transcription	Spleen	Spleen
12	chr1:169430200-169452600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr1:169430200-169452600	Weak transcription	NH-A	brain
14	chr1:169430200-169453200	Weak transcription	Esophagus	oesophagus
15	chr1:169430600-169452800	Weak transcription	Small Intestine	intestine
16	chr1:169434600-169452600	Weak transcription	Primary B cells from cord blood	blood
17	chr1:169435200-169452800	Weak transcription	Fetal Kidney	kidney
18	chr1:169437400-169452600	Weak transcription	HSMMtube	muscle
19	chr1:169437400-169452600	Weak transcription	Osteobl	bone
20	chr1:169437400-169452800	Weak transcription	Aorta	Aorta
21	chr1:169437400-169452800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:169437800-169452600	Weak transcription	Fetal Brain Female	brain
23	chr1:169438600-169452200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:169438600-169453200	Weak transcription	Fetal Lung	lung
25	chr1:169438800-169452600	Weak transcription	HSMM	muscle
26	chr1:169439600-169452600	Weak transcription	Primary T cells from cord blood	blood
27	chr1:169443000-169452800	Weak transcription	A549	lung
28	chr1:169443800-169452800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:169444200-169454000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:169444600-169452600	Weak transcription	Stomach Mucosa	stomach
31	chr1:169444600-169452800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:169446600-169453000	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:169446800-169452400	Weak transcription	Brain Anterior Caudate	brain
34	chr1:169446800-169452600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:169446800-169452600	Weak transcription	Fetal Muscle Leg	muscle
36	chr1:169446800-169452600	Weak transcription	Placenta	Placenta
37	chr1:169446800-169452600	Weak transcription	Fetal Stomach	stomach
38	chr1:169446800-169452800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:169446800-169452800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:169446800-169452800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:169446800-169452800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr1:169446800-169453000	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:169446800-169453000	Weak transcription	Fetal Thymus	thymus
44	chr1:169446800-169454200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:169446800-169454200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr1:169447000-169452200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:169447000-169452400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:169447000-169452600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:169447000-169452600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:169447000-169452600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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