Variant report

Variant	rs2076352
Chromosome Location	chr1:209801569-209801570
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	RAD21	chr1:209800646-209801574	SK-N-SH	brain:	n/a	chr1:209801168-209801180 chr1:209801170-209801180 chr1:209801169-209801182 chr1:209801173-209801187 chr1:209801166-209801185 chr1:209801172-209801186
2	SMC3	chr1:209800445-209801678	SK-N-SH	brain:	n/a	chr1:209801325-209801332 chr1:209801170-209801184
3	CTCF	chr1:209800510-209801654	SK-N-SH	brain:	n/a	chr1:209801175-209801183 chr1:209801163-209801184 chr1:209801168-209801186 chr1:209801170-209801183
4	CTCF	chr1:209801500-209801650	NB4	blood:	n/a	n/a
5	CTCF	chr1:209800612-209801661	A549	lung:	n/a	chr1:209801175-209801183 chr1:209801163-209801184 chr1:209801168-209801186 chr1:209801170-209801183
6	CTCF	chr1:209801420-209801570	Caco-2	colon:	n/a	n/a
7	CTCF	chr1:209801520-209801670	HCM	heart:	n/a	n/a
8	POLR2A	chr1:209798261-209801629	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr1:209801440-209801590	GM12874	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:209742477..209743064-chr1:209800705..209801620,3	K562	blood:
2	chr1:209800921..209801627-chr1:209920949..209921660,2	MCF-7	breast:
3	chr1:209800870..209803812-chr1:209809987..209812657,3	K562	blood:
4	chr1:209799563..209802450-chr1:209813916..209816529,2	K562	blood:
5	chr1:209749797..209750760-chr1:209800777..209801581,3	MCF-7	breast:
6	chr1:209800950..209802731-chr1:209813916..209816295,2	K562	blood:

Variant related genes	Relation type
MIR4260	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10489340	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12073223	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12089972	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12090288	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12403733	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12410975	1.00[CEU][hapmap];0.90[GIH][hapmap]
rs17014889	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17014906	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17014942	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17014955	1.00[CEU][hapmap];0.80[JPT][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17015006	0.82[MEX][hapmap]
rs2072937	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2072939	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072942	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2076219	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2076222	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2076232	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2076347	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2076348	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2076349	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[EUR][1000 genomes]
rs2076350	0.82[EUR][1000 genomes]
rs2229465	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2229466	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2235542	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2236889	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2236890	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2282734	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2282736	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2282737	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs36051870	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs58679997	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59815577	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60927005	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs714971	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209787200-209808400	Strong transcription	Placenta Amnion	Placenta Amnion
2	chr1:209787400-209816200	Strong transcription	NHEK	skin
3	chr1:209789000-209802800	Strong transcription	Hela-S3	cervix
4	chr1:209792400-209806400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:209793000-209801600	Enhancers	Ovary	ovary
6	chr1:209793600-209801600	Enhancers	Spleen	Spleen
7	chr1:209794800-209803200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:209795200-209804400	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:209797000-209801600	Enhancers	Right Ventricle	heart
10	chr1:209797800-209801600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr1:209797800-209803200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:209798000-209805200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:209798200-209801600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr1:209798400-209801600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:209798400-209801600	Enhancers	Left Ventricle	heart
16	chr1:209798600-209801600	Enhancers	Stomach Smooth Muscle	stomach
17	chr1:209798800-209801600	Enhancers	Brain Cingulate Gyrus	brain
18	chr1:209798800-209801600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr1:209798800-209801600	Strong transcription	Gastric	stomach
20	chr1:209799000-209801600	Enhancers	Brain Hippocampus Middle	brain
21	chr1:209799000-209801800	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr1:209799200-209801600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:209799400-209801600	Enhancers	Brain Anterior Caudate	brain
24	chr1:209799400-209806600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:209799600-209801600	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr1:209799600-209801600	Enhancers	Brain Angular Gyrus	brain
27	chr1:209799600-209803600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:209799800-209802000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:209799800-209814600	Strong transcription	Fetal Intestine Small	intestine
30	chr1:209800000-209801600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:209800000-209801600	Bivalent Enhancer	Placenta	Placenta
32	chr1:209800000-209801600	Enhancers	Lung	lung
33	chr1:209800000-209813200	Strong transcription	Fetal Intestine Large	intestine
34	chr1:209800200-209801600	Genic enhancers	Colonic Mucosa	Colon
35	chr1:209800200-209801600	Enhancers	Psoas Muscle	Psoas
36	chr1:209800600-209801600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
37	chr1:209800600-209805800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:209800800-209801600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:209800800-209801600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:209800800-209801600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:209800800-209801600	Flanking Active TSS	Brain Substantia Nigra	brain
42	chr1:209800800-209801600	Genic enhancers	Esophagus	oesophagus
43	chr1:209800800-209801600	Genic enhancers	Fetal Stomach	stomach
44	chr1:209800800-209803200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:209800800-209803200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:209800800-209804200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr1:209800800-209804800	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr1:209801000-209801600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
49	chr1:209801000-209802200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr1:209801000-209802600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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