Variant report

Variant	rs6720109
Chromosome Location	chr2:182674627-182674628
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:182673076..182675732-chr2:182690714..182692321,2	MCF-7	breast:
2	chr2:182673309..182675610-chr2:182753530..182756774,3	MCF-7	breast:
3	chr2:182653727..182657745-chr2:182674412..182677081,4	MCF-7	breast:
4	chr2:182674283..182676270-chr2:182679368..182682318,3	MCF-7	breast:
5	chr2:182674401..182676353-chr2:182754991..182757437,2	MCF-7	breast:
6	chr2:182674418..182676903-chr2:182677977..182680829,2	K562	blood:

Variant related genes	Relation type
ENSG00000260742	Chromatin interaction
ENSG00000138434	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10165936	1.00[CEU][hapmap]
rs10166812	0.85[JPT][hapmap]
rs10166975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10167581	0.83[YRI][hapmap]
rs10171629	0.81[AFR][1000 genomes]
rs10173114	1.00[CEU][hapmap]
rs10176061	1.00[CEU][hapmap]
rs10176613	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap]
rs10176757	1.00[CEU][hapmap]
rs10179363	1.00[CEU][hapmap]
rs10179547	1.00[CEU][hapmap]
rs10189187	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10191082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10199645	1.00[CEU][hapmap]
rs10200243	1.00[CEU][hapmap]
rs10201303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10203440	0.81[AFR][1000 genomes]
rs10210215	1.00[CEU][hapmap]
rs10221891	1.00[CEU][hapmap]
rs13391733	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13396152	0.80[YRI][hapmap];0.85[AFR][1000 genomes]
rs13401364	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13404156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13425734	1.00[CEU][hapmap]
rs1528024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs1528025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs1528026	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1528027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs16867498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16867509	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17456384	0.84[EUR][1000 genomes]
rs1881158	1.00[CEU][hapmap]
rs1881159	1.00[CEU][hapmap]
rs2059702	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2288330	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2303554	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2368224	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2368235	0.88[EUR][1000 genomes]
rs3731693	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs3815877	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs3815878	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs4597477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55732891	0.80[EUR][1000 genomes]
rs55758877	0.84[EUR][1000 genomes]
rs6433943	1.00[CEU][hapmap]
rs6707164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs6707654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6720702	1.00[CEU][hapmap]
rs6723011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735322	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6736341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6736766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6739707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6744556	0.80[EUR][1000 genomes]
rs6748354	1.00[CEU][hapmap]
rs6751464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751685	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6754192	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6754819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755017	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs73032623	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7557969	1.00[CEU][hapmap]
rs7562680	1.00[CEU][hapmap]
rs7580410	1.00[CEU][hapmap]
rs7600976	0.83[YRI][hapmap];0.85[AFR][1000 genomes]
rs7603721	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs7608942	1.00[CEU][hapmap]
rs9807949	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap]
rs9808112	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1001558	chr2:182590009-182732738	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv834478	chr2:182654811-182843201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6720109	LOC647288///LOC730587	trans	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182669200-182675600	Weak transcription	Thymus	Thymus
2	chr2:182669200-182676000	Weak transcription	Lung	lung
3	chr2:182669400-182675200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:182669400-182675600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:182669400-182675600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:182669400-182675800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:182669600-182675400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:182669800-182675600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:182670000-182675600	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:182670200-182675800	Weak transcription	Primary T cells from cord blood	blood
11	chr2:182670400-182675200	Weak transcription	NHEK	skin
12	chr2:182670600-182675400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:182670800-182675200	Weak transcription	Dnd41	blood
14	chr2:182670800-182675600	Weak transcription	Brain Substantia Nigra	brain
15	chr2:182671000-182675400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:182671000-182675400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr2:182671000-182675400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:182671000-182675400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:182671000-182675400	Weak transcription	HMEC	breast
20	chr2:182671000-182675400	Weak transcription	HSMM	muscle
21	chr2:182671000-182675400	Weak transcription	HSMMtube	muscle
22	chr2:182671000-182675400	Weak transcription	K562	blood
23	chr2:182671000-182675400	Weak transcription	NHDF-Ad	bronchial
24	chr2:182671000-182675600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:182671000-182675600	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:182671000-182675600	Weak transcription	Fetal Kidney	kidney
27	chr2:182671000-182675600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:182671000-182675800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:182671000-182675800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:182671000-182675800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:182671000-182675800	Weak transcription	Adipose Nuclei	Adipose
32	chr2:182671000-182675800	Weak transcription	Pancreas	Pancrea
33	chr2:182671000-182676000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr2:182671000-182676000	Weak transcription	Left Ventricle	heart
35	chr2:182671000-182676000	Weak transcription	Right Atrium	heart
36	chr2:182671000-182678400	Weak transcription	Aorta	Aorta
37	chr2:182671200-182675200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr2:182671200-182675400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:182671200-182675400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:182671200-182675400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr2:182671200-182675400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:182671200-182675400	Weak transcription	Osteobl	bone
43	chr2:182671200-182675600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr2:182671200-182675600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:182671200-182675600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:182671200-182675600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:182671200-182678800	Weak transcription	NHLF	lung
48	chr2:182671200-182682600	Weak transcription	Fetal Stomach	stomach
49	chr2:182673400-182674800	Enhancers	Stomach Mucosa	stomach
50	chr2:182673400-182674800	Enhancers	A549	lung

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