Variant report

Variant	rs12401878
Chromosome Location	chr1:247006314-247006315
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247005474..247007845-chr1:247009959..247011844,2	K562	blood:
2	chr1:246999464..247001183-chr1:247004017..247007456,3	MCF-7	breast:
3	chr1:247000678..247002401-chr1:247004834..247006838,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10802451	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10924861	0.90[CEU][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs11576429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12031687	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12048921	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12401831	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12403415	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12410563	1.00[CEU][hapmap];0.93[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28727999	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971286	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55783683	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56070865	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61853987	0.84[EUR][1000 genomes]
rs61853988	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61853995	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9633321	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][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	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers 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	52 gene(s)	inside rSNPs	diseases
6	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv1810844	chr1:246988018-247054824	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
9	esv3335090	chr1:247006271-247006723	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12401878	AHCTF1	Cis_1M	lymphoblastoid	RTeQTL
rs12401878	CEP170	cis	parietal	SCAN
rs12401878	ZNF669	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246989200-247011200	Weak transcription	Fetal Kidney	kidney
2	chr1:246999200-247010000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:246999800-247007600	Weak transcription	Right Ventricle	heart
4	chr1:247000200-247020200	Weak transcription	Spleen	Spleen
5	chr1:247000600-247007800	Weak transcription	Fetal Brain Female	brain
6	chr1:247001400-247012000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:247001400-247016400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:247001400-247020000	Weak transcription	Brain Substantia Nigra	brain
9	chr1:247002000-247038200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:247002200-247031400	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:247002200-247033800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:247002200-247034200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:247002200-247082400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr1:247002400-247081000	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr1:247002800-247006800	Strong transcription	Placenta	Placenta
16	chr1:247002800-247009200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:247002800-247010000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:247002800-247032600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:247002800-247043200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:247003000-247007400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:247003000-247007800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:247003000-247011000	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:247003000-247015200	Weak transcription	Fetal Heart	heart
24	chr1:247003000-247015200	Weak transcription	NHLF	lung
25	chr1:247003000-247018600	Weak transcription	Fetal Brain Male	brain
26	chr1:247003200-247009000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:247003200-247010000	Weak transcription	Aorta	Aorta
28	chr1:247003200-247012000	Weak transcription	Psoas Muscle	Psoas
29	chr1:247003200-247015200	Weak transcription	Esophagus	oesophagus
30	chr1:247003200-247020400	Weak transcription	Gastric	stomach
31	chr1:247003200-247029200	Strong transcription	Fetal Thymus	thymus
32	chr1:247003200-247042200	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:247003200-247042800	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:247003400-247010800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:247003400-247022600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr1:247003400-247043000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:247003400-247044600	Strong transcription	Dnd41	blood
38	chr1:247004000-247009400	Strong transcription	Osteobl	bone
39	chr1:247004000-247009800	Strong transcription	NHEK	skin
40	chr1:247004000-247013600	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:247004000-247022200	Strong transcription	Fetal Intestine Large	intestine
42	chr1:247004000-247040800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:247004000-247041200	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr1:247004000-247042800	Strong transcription	Primary T cells from cord blood	blood
45	chr1:247004000-247053600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:247004200-247006600	Strong transcription	Fetal Intestine Small	intestine
47	chr1:247004200-247006600	Strong transcription	Fetal Stomach	stomach
48	chr1:247004200-247006800	Strong transcription	Colon Smooth Muscle	Colon
49	chr1:247004200-247007400	Weak transcription	Lung	lung
50	chr1:247004200-247008200	Strong transcription	Duodenum Mucosa	Duodenum

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