Variant report

Variant	rs6427232
Chromosome Location	chr1:170041721-170041722
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:170032663..170035514-chr1:170040847..170042460,2	MCF-7	breast:
2	chr1:170037046..170038634-chr1:170041259..170042880,2	K562	blood:

Variant related genes	Relation type
ENSG00000075945	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10919283	0.93[YRI][hapmap]
rs11584929	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589247	0.93[YRI][hapmap]
rs1330377	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1541160	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16862745	0.93[YRI][hapmap]
rs2050628	0.93[YRI][hapmap]
rs2065950	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2474708	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28441321	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476269	1.00[CEU][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs522444	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527261	0.95[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541655	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541896	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546894	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs571398	1.00[CEU][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614044	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628436	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427230	0.92[YRI][hapmap]
rs648576	1.00[YRI][hapmap]
rs6668310	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6694304	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs693673	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72715936	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539241	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427175	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973015	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1014033	chr1:169968488-170453021	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats 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	18 gene(s)	inside rSNPs	diseases
2	nsv535200	chr1:169968488-170453021	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169952400-170043000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:170018200-170042400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:170019000-170042600	Weak transcription	Thymus	Thymus
4	chr1:170019200-170042400	Weak transcription	Fetal Lung	lung
5	chr1:170032800-170042400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:170032800-170042600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:170033800-170042400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:170036400-170042200	Weak transcription	NHEK	skin
9	chr1:170036600-170043000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr1:170036800-170042600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:170037000-170042600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:170037000-170042800	Weak transcription	Right Atrium	heart
13	chr1:170037000-170043000	Weak transcription	Left Ventricle	heart
14	chr1:170037000-170043200	Weak transcription	Small Intestine	intestine
15	chr1:170037200-170042000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:170037200-170042600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:170037200-170042600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr1:170037200-170042600	Weak transcription	Fetal Thymus	thymus
19	chr1:170037200-170042600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:170037200-170042600	Weak transcription	HepG2	liver
21	chr1:170037200-170043200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:170037400-170042000	Weak transcription	K562	blood
23	chr1:170037400-170043000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr1:170037800-170042000	Weak transcription	Adipose Nuclei	Adipose
25	chr1:170037800-170042600	Weak transcription	Fetal Heart	heart
26	chr1:170038000-170043200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:170038400-170042200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:170038600-170042000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:170038600-170042000	Weak transcription	NHLF	lung
30	chr1:170038600-170042600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr1:170038600-170043000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr1:170038600-170043000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:170039400-170042600	Weak transcription	Fetal Stomach	stomach
34	chr1:170040000-170042600	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr1:170040000-170043000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:170040600-170042400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:170040800-170042400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:170040800-170042600	Enhancers	Fetal Brain Male	brain
39	chr1:170041000-170042200	Enhancers	Fetal Brain Female	brain
40	chr1:170041000-170042400	Weak transcription	Brain Germinal Matrix	brain
41	chr1:170041000-170042600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr1:170041000-170042600	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr1:170041000-170042600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:170041000-170042600	Weak transcription	Aorta	Aorta
45	chr1:170041000-170042600	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:170041000-170043000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:170041000-170043200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:170041000-170044200	Active TSS	GM12878-XiMat	blood
49	chr1:170041200-170042600	Weak transcription	Liver	Liver
50	chr1:170041200-170043000	Enhancers	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links