Variant report

Variant	rs12410327
Chromosome Location	chr1:227443245-227443246
allele	C/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	RCOR1	chr1:227442866-227443361	K562	blood:	n/a	n/a
2	GATA3	chr1:227442786-227443332	SK-N-SH	brain:	n/a	chr1:227442857-227442867
3	JUND	chr1:227442994-227443438	K562	blood:	n/a	n/a
4	GATA3	chr1:227442662-227443412	MCF-7	breast:	n/a	chr1:227442857-227442867
5	CBX3	chr1:227443043-227443436	K562	blood:	n/a	n/a
6	GATA3	chr1:227442642-227443345	MCF-7	breast:	n/a	chr1:227442857-227442867
7	FOSL1	chr1:227443147-227443418	K562	blood:	n/a	n/a
8	JUND	chr1:227443215-227443327	H1-hESC	embryonic stem cell:	n/a	n/a
9	JUND	chr1:227443170-227443420	H1-hESC	embryonic stem cell:	n/a	n/a
10	HDAC2	chr1:227442807-227443251	MCF-7	breast:	n/a	chr1:227443185-227443199
11	E2F4	chr1:227443173-227443290	MCF10A-Er-Src	breast:	n/a	n/a
12	GATA3	chr1:227442656-227443337	SK-N-SH	brain:	n/a	chr1:227442857-227442867

No.	Distal block	Cell Line	Cell type
1	chr1:227442920..227447581-chr1:227503938..227508329,6	K562	blood:
2	chr1:227441285..227444497-chr1:227452902..227455834,3	K562	blood:
3	chr1:227442920..227445120-chr1:227505112..227507012,2	K562	blood:

Variant related genes	Relation type
CDC42BPA	TF binding region
ENSG00000236636	Chromatin interaction
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1015815	0.96[EUR][1000 genomes]
rs1015816	0.94[EUR][1000 genomes]
rs10495258	0.80[AMR][1000 genomes]
rs10495263	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs10916109	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10916114	0.98[EUR][1000 genomes]
rs11799413	1.00[CEU][hapmap]
rs11801994	0.94[EUR][1000 genomes]
rs11803590	0.94[EUR][1000 genomes]
rs11803761	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11805298	0.90[EUR][1000 genomes]
rs11806511	0.94[EUR][1000 genomes]
rs11806937	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11808928	0.94[EUR][1000 genomes]
rs11810328	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11811358	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12402456	0.94[EUR][1000 genomes]
rs12403650	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12403833	0.91[CEU][hapmap];0.80[AMR][1000 genomes]
rs12403986	0.94[EUR][1000 genomes]
rs12404627	0.80[AMR][1000 genomes]
rs12405363	0.95[EUR][1000 genomes]
rs12405878	1.00[CEU][hapmap]
rs12407061	0.80[AMR][1000 genomes]
rs12408913	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12410337	1.00[CEU][hapmap]
rs12410460	1.00[CEU][hapmap]
rs12741049	0.89[EUR][1000 genomes]
rs1464076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1464077	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1513602	0.94[EUR][1000 genomes]
rs1513603	0.90[EUR][1000 genomes]
rs1546557	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1606549	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16846972	1.00[CEU][hapmap]
rs16846985	1.00[CEU][hapmap]
rs16847014	1.00[CEU][hapmap]
rs16847035	1.00[CEU][hapmap]
rs16847098	1.00[CEU][hapmap]
rs16847107	1.00[CEU][hapmap]
rs16847492	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs16847634	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17605533	0.80[AMR][1000 genomes]
rs17613166	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1877622	1.00[CEU][hapmap]
rs1888831	1.00[CEU][hapmap]
rs34263105	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34400564	0.90[EUR][1000 genomes]
rs34953255	0.86[AMR][1000 genomes]
rs41270149	0.94[EUR][1000 genomes]
rs4255349	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4282782	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4300186	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4354510	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4434814	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4437846	0.96[EUR][1000 genomes]
rs4518864	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4543764	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4551563	0.80[AMR][1000 genomes]
rs55805110	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55882852	0.94[EUR][1000 genomes]
rs55946024	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57276421	0.94[EUR][1000 genomes]
rs57758974	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58489467	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59116340	0.90[EUR][1000 genomes]
rs59121440	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59859849	0.94[EUR][1000 genomes]
rs60068245	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60235610	0.94[EUR][1000 genomes]
rs60742095	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60958272	0.95[EUR][1000 genomes]
rs61081394	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61522132	0.90[EUR][1000 genomes]
rs6659506	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6668367	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6675521	1.00[YRI][hapmap]
rs73088658	0.90[EUR][1000 genomes]
rs73090612	0.90[EUR][1000 genomes]
rs73094351	0.92[EUR][1000 genomes]
rs73094393	0.94[EUR][1000 genomes]
rs73094400	0.95[EUR][1000 genomes]
rs73096317	0.95[EUR][1000 genomes]
rs73096350	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73096353	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73096358	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73096374	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73098390	0.95[EUR][1000 genomes]
rs73098398	0.95[EUR][1000 genomes]
rs73102307	0.95[EUR][1000 genomes]
rs7413768	0.80[AMR][1000 genomes]
rs74140153	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7515739	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7519099	0.93[EUR][1000 genomes]
rs7526283	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7534286	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7535010	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7539037	0.90[EUR][1000 genomes]
rs7539750	0.90[EUR][1000 genomes]
rs7542505	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7544923	0.93[EUR][1000 genomes]
rs7545775	0.95[EUR][1000 genomes]
rs7551556	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227414000-227459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:227414200-227453800	Weak transcription	HSMM	muscle
3	chr1:227415800-227456800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:227425400-227445200	Weak transcription	Osteobl	bone
5	chr1:227431600-227486200	Weak transcription	NHDF-Ad	bronchial
6	chr1:227432000-227459200	Weak transcription	Fetal Lung	lung
7	chr1:227432200-227455400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:227432600-227448000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:227432800-227446000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:227432800-227455600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:227433000-227446000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:227433000-227446000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:227433000-227469000	Weak transcription	Aorta	Aorta
14	chr1:227433200-227452800	Weak transcription	Ovary	ovary
15	chr1:227434000-227444200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:227434000-227446800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:227434000-227447000	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:227434000-227453400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:227434200-227455400	Weak transcription	Left Ventricle	heart
20	chr1:227434200-227455400	Weak transcription	Right Ventricle	heart
21	chr1:227434200-227455800	Weak transcription	Adipose Nuclei	Adipose
22	chr1:227434400-227443400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:227434400-227446000	Weak transcription	Brain Substantia Nigra	brain
24	chr1:227434600-227468800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:227434800-227458400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:227435000-227457000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:227435600-227453600	Weak transcription	Fetal Intestine Small	intestine
28	chr1:227437800-227443400	Weak transcription	Fetal Brain Female	brain
29	chr1:227438800-227448000	Weak transcription	Psoas Muscle	Psoas
30	chr1:227438800-227449400	Weak transcription	Right Atrium	heart
31	chr1:227440000-227456600	Weak transcription	HepG2	liver
32	chr1:227440200-227456800	Weak transcription	HUVEC	blood vessel
33	chr1:227441200-227450000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:227441800-227449600	Weak transcription	A549	lung
35	chr1:227441800-227452000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:227442400-227443400	Enhancers	K562	blood
37	chr1:227442400-227449600	Weak transcription	Brain Angular Gyrus	brain
38	chr1:227442800-227443400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:227443000-227443400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:227443200-227446800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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