Variant report

Variant	rs2255541
Chromosome Location	chr7:2843161-2843162
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2798496..2801749-chr7:2841464..2845020,4	MCF-7	breast:
2	chr7:2842591..2845242-chr7:2882399..2885684,4	MCF-7	breast:
3	chr7:2836297..2839698-chr7:2841908..2844688,4	K562	blood:
4	chr7:2837885..2839516-chr7:2842777..2844546,2	MCF-7	breast:
5	chr7:2835435..2836946-chr7:2841542..2843166,2	MCF-7	breast:
6	chr7:2834690..2837534-chr7:2842930..2845047,2	MCF-7	breast:
7	chr7:2832115..2834108-chr7:2841664..2843716,2	MCF-7	breast:
8	chr7:2840989..2843373-chr7:2899244..2901944,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146535	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1182206	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2057918	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs208345	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs208346	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs208354	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs208356	0.91[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.83[ASN][1000 genomes]
rs208358	0.81[YRI][hapmap]
rs2251718	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2255782	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2258709	0.82[CHB][hapmap]
rs2258960	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2266923	0.87[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2266925	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2527682	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2527686	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs2527689	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2533886	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs2533888	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs2644272	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2644276	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2644306	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs2644311	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3846992	0.83[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs709280	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs709281	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs757786	0.82[CHB][hapmap]
rs757789	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs757790	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7790322	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs798501	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798504	0.81[EUR][1000 genomes]
rs798509	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs798515	0.89[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs798516	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs798517	0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798519	0.84[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798520	0.80[ASN][1000 genomes]
rs798521	0.91[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798522	0.86[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs798523	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs798524	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798525	0.83[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798527	0.91[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs798529	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs798530	0.86[CEU][hapmap];0.91[CHB][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs798532	0.86[CHB][hapmap]
rs798549	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029250	chr7:2722737-2881021	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv538652	chr7:2722737-2881021	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1015700	chr7:2753965-2945848	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1022612	chr7:2789555-3019200	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1018162	chr7:2817460-2891181	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv538655	chr7:2817460-2891181	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2255541	GNA12	cis	Artery Tibial	GTEx
rs2255541	GNA12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2834600-2847800	Weak transcription	Liver	Liver
2	chr7:2836600-2844600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr7:2837000-2850600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr7:2838600-2844200	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr7:2839400-2843600	Enhancers	Dnd41	blood
6	chr7:2839400-2848600	Enhancers	Fetal Heart	heart
7	chr7:2839400-2850800	Weak transcription	Primary B cells from cord blood	blood
8	chr7:2839600-2843400	Enhancers	Fetal Muscle Leg	muscle
9	chr7:2839600-2845000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr7:2840000-2844200	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr7:2840000-2844200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr7:2840200-2845200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr7:2840400-2843200	Enhancers	HSMMtube	muscle
14	chr7:2840400-2846200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr7:2840600-2844000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:2840800-2843400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr7:2840800-2843400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr7:2840800-2843600	Enhancers	Colon Smooth Muscle	Colon
19	chr7:2841000-2843200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr7:2841000-2843200	Enhancers	Brain Anterior Caudate	brain
21	chr7:2841000-2843400	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr7:2841000-2844200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr7:2841000-2844200	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr7:2841000-2850200	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr7:2841200-2845000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:2841200-2847400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr7:2841400-2843400	Enhancers	NHDF-Ad	bronchial
28	chr7:2841400-2843600	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr7:2841400-2843600	Weak transcription	K562	blood
30	chr7:2841400-2846400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr7:2841400-2847000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr7:2841400-2847400	Weak transcription	GM12878-XiMat	blood
33	chr7:2841400-2847800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr7:2842000-2844000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr7:2842000-2844200	Enhancers	H1 Cell Line	embryonic stem cell
36	chr7:2842200-2843200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr7:2842200-2843200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr7:2842200-2843200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr7:2842200-2843200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr7:2842200-2843200	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr7:2842200-2843200	Flanking Active TSS	Fetal Intestine Small	intestine
42	chr7:2842200-2843200	Flanking Active TSS	Fetal Lung	lung
43	chr7:2842200-2843200	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr7:2842200-2843200	Flanking Active TSS	NHLF	lung
45	chr7:2842200-2843400	Enhancers	Brain Cingulate Gyrus	brain
46	chr7:2842200-2843400	Enhancers	Brain Hippocampus Middle	brain
47	chr7:2842200-2843400	Flanking Active TSS	NHEK	skin
48	chr7:2842200-2844200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr7:2842200-2844200	Enhancers	Small Intestine	intestine
50	chr7:2842200-2844400	Flanking Active TSS	HepG2	liver

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