Variant report

Variant	rs6684956
Chromosome Location	chr1:225649159-225649160
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225626720..225628379-chr1:225647904..225650755,2	K562	blood:
2	chr1:225648477..225651119-chr1:225966156..225969061,2	K562	blood:
3	chr1:225637801..225642696-chr1:225647950..225650939,4	K562	blood:
4	chr1:225632782..225636036-chr1:225646050..225649453,3	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10449249	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10915829	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11377355	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12022013	1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12026034	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12031651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12037289	0.85[ASN][1000 genomes]
rs12038373	0.82[MEX][hapmap]
rs12042273	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12239415	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12405879	0.83[ASN][1000 genomes]
rs12405904	0.83[ASN][1000 genomes]
rs1340866	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1340870	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1340871	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1340872	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16845000	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2184778	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2185531	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2297747	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28620013	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3766931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3795443	1.00[CHB][hapmap]
rs4129816	0.84[ASN][1000 genomes]
rs55751087	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56169721	0.85[ASN][1000 genomes]
rs58269599	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59912270	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61333083	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6674621	1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[ASN][1000 genomes]
rs6681559	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6684314	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6694938	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74146931	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74146994	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74149835	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs74149844	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7539651	0.88[GIH][hapmap]
rs7543444	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats 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	19 gene(s)	inside rSNPs	diseases
3	esv34905	chr1:225631404-225676582	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6684956	LBR	cis	Esophagus Muscularis	GTEx
rs6684956	LBR	cis	Artery Tibial	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225636200-225650000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:225642400-225650800	Weak transcription	Right Atrium	heart
3	chr1:225642400-225653000	Weak transcription	Primary B cells from cord blood	blood
4	chr1:225642400-225655200	Weak transcription	Small Intestine	intestine
5	chr1:225642600-225655000	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:225642800-225650000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:225642800-225652800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:225643000-225650400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:225643000-225651000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:225645800-225649400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:225646400-225653600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:225647000-225649200	Enhancers	NHEK	skin
13	chr1:225647000-225649400	Enhancers	Muscle Satellite Cultured Cells	--
14	chr1:225647000-225649400	Enhancers	HSMM	muscle
15	chr1:225647000-225651600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr1:225647000-225651600	Enhancers	Fetal Muscle Leg	muscle
17	chr1:225647000-225653600	Enhancers	Esophagus	oesophagus
18	chr1:225647000-225654600	Enhancers	Fetal Thymus	thymus
19	chr1:225647000-225654800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:225647200-225649600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:225647200-225649800	Enhancers	Thymus	Thymus
22	chr1:225647200-225651600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr1:225647400-225651200	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr1:225647400-225654800	Enhancers	Primary T cells fromperipheralblood	blood
25	chr1:225647600-225649200	Enhancers	Fetal Muscle Trunk	muscle
26	chr1:225647600-225649400	Enhancers	Dnd41	blood
27	chr1:225647600-225649600	Enhancers	Duodenum Mucosa	Duodenum
28	chr1:225647600-225650200	Enhancers	Spleen	Spleen
29	chr1:225647600-225650200	Enhancers	A549	lung
30	chr1:225647600-225652000	Enhancers	Fetal Stomach	stomach
31	chr1:225647600-225653800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:225647800-225649200	Enhancers	Primary T cells from cord blood	blood
33	chr1:225647800-225649600	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr1:225647800-225649600	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr1:225647800-225649800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:225647800-225649800	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr1:225647800-225650200	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr1:225647800-225653400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:225648000-225649200	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr1:225648000-225649600	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr1:225648000-225649600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr1:225648000-225649800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr1:225648000-225650200	Flanking Active TSS	Rectal Smooth Muscle	rectum
44	chr1:225648000-225651400	Enhancers	Fetal Brain Male	brain
45	chr1:225648000-225652600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:225648200-225649200	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr1:225648200-225649200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr1:225648200-225649200	Flanking Active TSS	Hela-S3	cervix
49	chr1:225648200-225649800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:225648200-225651000	Weak transcription	Fetal Intestine Small	intestine

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