Variant report

Variant	rs1888991
Chromosome Location	chr1:197110822-197110823
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr1:197110722-197111199	T-47D	breast:	n/a	chr1:197111103-197111115
2	ZNF143	chr1:197110720-197110857	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:197110811-197111956	MCF10A-Er-Src	breast:	n/a	n/a
4	RCOR1	chr1:197110725-197110925	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr1:197110714-197112179	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr1:197110354-197112735	K562	blood:	n/a	n/a
7	ZKSCAN1	chr1:197110724-197111159	Hela-S3	cervix:	n/a	n/a
8	CUX1	chr1:197110709-197110935	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:197110180..197113762-chr1:197163844..197167381,3	K562	blood:
2	chr1:197063964..197065535-chr1:197110090..197112434,2	K562	blood:
3	chr1:197108980..197111975-chr1:197160260..197161833,2	K562	blood:
4	chr1:197082888..197084637-chr1:197110135..197112878,2	K562	blood:
5	chr1:197088400..197091064-chr1:197110423..197113146,2	K562	blood:
6	chr1:197080735..197084388-chr1:197109840..197112878,3	K562	blood:
7	chr1:197100050..197103962-chr1:197110434..197115621,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000235748	TF binding region

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1034162	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10732295	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs10733087	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10737687	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10754213	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10754214	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10754215	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10801587	0.93[EUR][1000 genomes]
rs10801588	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10801590	0.93[EUR][1000 genomes]
rs10801591	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10922165	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10922166	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10922169	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1115246	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1115247	0.87[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1170880	0.87[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap]
rs1170881	0.87[CEU][hapmap]
rs12039586	0.86[EUR][1000 genomes]
rs12092294	0.87[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap]
rs12677	0.82[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12731209	0.87[CEU][hapmap]
rs1332662	0.87[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1332663	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1332669	0.89[EUR][1000 genomes]
rs1412631	0.87[CEU][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs1412632	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1412633	0.93[EUR][1000 genomes]
rs1412634	0.87[CEU][hapmap];0.93[EUR][1000 genomes]
rs1412639	0.89[EUR][1000 genomes]
rs1537319	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1556763	0.94[ASW][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs1571964	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1576878	0.89[EUR][1000 genomes]
rs1627765	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1759006	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1759007	0.93[EUR][1000 genomes]
rs1759008	0.93[EUR][1000 genomes]
rs1759009	0.93[EUR][1000 genomes]
rs1759013	0.93[EUR][1000 genomes]
rs1794003	0.93[EUR][1000 genomes]
rs1794010	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1953064	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2026429	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2151133	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2151134	0.86[CEU][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2151135	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336595	0.89[EUR][1000 genomes]
rs2336597	0.89[EUR][1000 genomes]
rs3891964	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4342879	0.87[EUR][1000 genomes]
rs4350226	0.87[EUR][1000 genomes]
rs4556392	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4915148	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4915156	0.93[EUR][1000 genomes]
rs4915313	0.93[EUR][1000 genomes]
rs4915315	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4915316	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4915327	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4915337	0.87[CEU][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4915345	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4915378	1.00[GIH][hapmap]
rs4915379	0.84[ASW][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
rs5997	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6003	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6428387	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6656858	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6671696	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6677082	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6679189	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6680497	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6685259	0.93[EUR][1000 genomes]
rs6695300	1.00[EUR][1000 genomes]
rs6703400	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7411719	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7516700	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7520503	1.00[GIH][hapmap];0.93[TSI][hapmap]
rs7534353	0.87[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7539642	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7541429	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7542397	0.87[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7554757	0.84[EUR][1000 genomes]
rs857017	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs857020	0.86[EUR][1000 genomes]
rs857021	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs857022	0.89[EUR][1000 genomes]
rs857023	0.89[EUR][1000 genomes]
rs857026	0.89[EUR][1000 genomes]
rs857027	0.89[EUR][1000 genomes]
rs865071	0.88[EUR][1000 genomes]
rs877897	0.87[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs928439	0.87[CEU][hapmap]
rs928440	0.87[CEU][hapmap]
rs9427660	0.87[CEU][hapmap]
rs9427661	0.87[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap]
rs9427662	0.87[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap]
rs9427942	0.87[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap]
rs9726778	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758990	chr1:196590837-197169772	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats 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	15 gene(s)	inside rSNPs	diseases
3	nsv427897	chr1:196590837-197169772	Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv2757767	chr1:196977799-197169772	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv873070	chr1:197079671-197165014	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv873071	chr1:197079671-197187605	Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv873072	chr1:197079671-197221248	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv548871	chr1:197106604-197168233	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv873073	chr1:197107074-197221248	Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers 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 target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197052200-197114200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:197054200-197113600	Weak transcription	Fetal Kidney	kidney
3	chr1:197055000-197114200	Weak transcription	Primary B cells from cord blood	blood
4	chr1:197073000-197115000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:197074000-197115000	Weak transcription	Fetal Brain Male	brain
6	chr1:197077000-197114200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:197085800-197111000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:197095800-197114400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:197100400-197112800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:197100400-197113600	Weak transcription	HSMM	muscle
11	chr1:197100600-197111200	Weak transcription	NH-A	brain
12	chr1:197100600-197113000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:197100800-197114200	Weak transcription	Fetal Intestine Large	intestine
14	chr1:197101200-197113000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:197102600-197113800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:197104600-197113600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:197105400-197113600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr1:197106200-197112600	Strong transcription	Fetal Thymus	thymus
19	chr1:197106200-197113000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:197106400-197113400	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:197106600-197113000	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:197106800-197113000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:197107800-197113600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:197107800-197113800	Weak transcription	Fetal Intestine Small	intestine
25	chr1:197108000-197112400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:197108000-197113800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr1:197108000-197115000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:197108400-197111000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:197108400-197111400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:197108400-197113400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:197108400-197113600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:197108600-197112400	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr1:197108600-197113600	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:197108600-197113800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr1:197108600-197114000	Weak transcription	Fetal Stomach	stomach
36	chr1:197108600-197115000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:197108600-197115200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:197108800-197111400	Strong transcription	HMEC	breast
39	chr1:197109000-197111600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:197109000-197112800	Genic enhancers	Hela-S3	cervix
41	chr1:197109200-197111000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:197109200-197111600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:197109200-197112400	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr1:197109400-197111000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:197109400-197115000	Weak transcription	HSMMtube	muscle
46	chr1:197109600-197111200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:197109600-197111800	Enhancers	HepG2	liver
48	chr1:197109600-197112600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:197109600-197113600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:197109600-197113600	Active TSS	GM12878-XiMat	blood

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