Variant report

Variant	rs6427227
Chromosome Location	chr1:169848791-169848792
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169846979..169849303-chr1:169851464..169854908,3	K562	blood:
2	chr1:169848453..169850292-chr1:169861471..169863318,2	MCF-7	breast:
3	chr1:169846941..169849701-chr1:169857998..169859525,2	MCF-7	breast:
4	chr1:169847953..169852057-chr1:169858381..169863040,5	MCF-7	breast:
5	chr1:169846456..169849390-chr1:169863296..169865489,2	MCF-7	breast:
6	chr1:169846082..169850359-chr1:169859892..169864668,5	K562	blood:
7	chr1:169847146..169850317-chr1:169850331..169854277,4	K562	blood:

Variant related genes	Relation type
ENSG00000000457	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10733054	0.80[JPT][hapmap]
rs10737549	0.84[CHB][hapmap];0.84[JPT][hapmap];0.87[YRI][hapmap];0.87[ASN][1000 genomes]
rs10737550	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10737551	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10800479	0.84[ASN][1000 genomes]
rs10800480	0.86[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.84[ASN][1000 genomes]
rs10800481	0.86[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.86[ASN][1000 genomes]
rs10800483	0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.89[ASN][1000 genomes]
rs10800484	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10800486	0.83[YRI][hapmap];0.90[AFR][1000 genomes]
rs10919239	0.80[JPT][hapmap]
rs10919245	0.83[ASN][1000 genomes]
rs10919248	0.86[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.84[ASN][1000 genomes]
rs10919251	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10919257	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10919263	0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12047487	0.93[CEU][hapmap];0.86[CHB][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12133843	0.90[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1883436	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2056981	0.86[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2143122	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2179396	0.86[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2205845	0.80[YRI][hapmap]
rs2281039	0.83[ASN][1000 genomes]
rs2294322	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2294496	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2420512	0.90[ASN][1000 genomes]
rs2901179	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3753308	0.87[YRI][hapmap];0.90[AFR][1000 genomes]
rs3766132	0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs3766134	0.83[ASN][1000 genomes]
rs3766137	0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3766142	0.90[ASN][1000 genomes]
rs3766144	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766148	0.90[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.90[ASN][1000 genomes]
rs3766151	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs3766154	0.84[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3766155	1.00[CEU][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4376791	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4508080	0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4614317	0.86[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.85[ASN][1000 genomes]
rs4615900	0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs4656196	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4656197	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4656199	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4656200	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4656721	0.85[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4656724	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4656725	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs508063	0.85[CEU][hapmap]
rs603246	0.82[CEU][hapmap]
rs6427217	0.84[JPT][hapmap]
rs6427220	0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6427224	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6427225	0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6427226	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6427228	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6656965	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6664099	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6668114	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6669794	0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6671752	0.93[ASN][1000 genomes]
rs6680508	0.81[JPT][hapmap]
rs6680650	0.84[ASN][1000 genomes]
rs6680938	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6682137	0.89[ASN][1000 genomes]
rs6682835	0.85[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6683056	0.90[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6684481	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6687377	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6702969	0.98[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs717481	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs732185	0.81[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs7519364	0.85[ASN][1000 genomes]
rs7521700	1.00[CEU][hapmap];0.80[YRI][hapmap];0.90[EUR][1000 genomes]
rs7525259	0.90[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7530237	0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs7545011	0.83[ASN][1000 genomes]
rs9287097	0.90[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6427227	C1orf112	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:169805400-169848800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:169806600-169860000	Weak transcription	Stomach Mucosa	stomach
4	chr1:169833800-169860200	Weak transcription	HMEC	breast
5	chr1:169842200-169857400	Weak transcription	Fetal Brain Male	brain
6	chr1:169842400-169848800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:169842400-169850800	Weak transcription	Esophagus	oesophagus
8	chr1:169842400-169851000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:169842400-169851000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:169842400-169855600	Weak transcription	Brain Angular Gyrus	brain
11	chr1:169842400-169860000	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:169842600-169854800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:169843000-169850200	Weak transcription	Colonic Mucosa	Colon
14	chr1:169843000-169851000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:169843600-169855000	Weak transcription	NHEK	skin
16	chr1:169843800-169850800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:169844000-169851200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:169844000-169851200	Weak transcription	Pancreas	Pancrea
19	chr1:169844000-169860000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:169844400-169857400	Weak transcription	K562	blood
21	chr1:169844800-169851200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:169844800-169854600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:169844800-169855400	Weak transcription	Hela-S3	cervix
24	chr1:169844800-169856000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:169844800-169860600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:169845000-169854000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:169845200-169850800	Weak transcription	Brain Germinal Matrix	brain
28	chr1:169845200-169850800	Weak transcription	Lung	lung
29	chr1:169845200-169851000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:169845200-169851000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:169845200-169853800	Weak transcription	Fetal Kidney	kidney
32	chr1:169845200-169854400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr1:169845200-169855000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr1:169845200-169857200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:169845200-169857200	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:169845200-169857400	Weak transcription	HUVEC	blood vessel
37	chr1:169845200-169861400	Weak transcription	Right Ventricle	heart
38	chr1:169845200-169861400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:169845400-169853400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:169845400-169859600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr1:169845400-169860000	Weak transcription	Psoas Muscle	Psoas
42	chr1:169845400-169861400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:169845600-169850600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:169845600-169855000	Weak transcription	Fetal Brain Female	brain
45	chr1:169845800-169855600	Weak transcription	A549	lung
46	chr1:169846000-169854600	Weak transcription	HSMMtube	muscle
47	chr1:169846000-169858000	Weak transcription	Small Intestine	intestine
48	chr1:169846600-169851000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:169846600-169851000	Weak transcription	Fetal Intestine Small	intestine
50	chr1:169846600-169851000	Weak transcription	Fetal Stomach	stomach

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