Variant report

Variant	rs218900
Chromosome Location	chr8:90730906-90730907
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:90729414..90732733-chr8:91011369..91014401,3	MCF-7	breast:
2	chr8:90728421..90731322-chr8:90768426..90770911,3	MCF-7	breast:
3	chr8:90730221..90731273-chr8:91007539..91008842,5	MCF-7	breast:
4	chr8:90730601..90732192-chr8:90769579..90771493,2	K562	blood:
5	chr8:90728791..90734507-chr8:90768671..90772991,6	MCF-7	breast:
6	chr8:90730784..90732523-chr8:90913744..90915377,2	MCF-7	breast:
7	chr8:90730206..90731189-chr8:90996034..90997277,6	MCF-7	breast:
8	chr8:90730227..90732540-chr8:90735572..90739536,4	MCF-7	breast:
9	chr8:90730369..90731173-chr8:91007945..91008879,2	K562	blood:
10	chr8:90727781..90733734-chr8:90995200..90998684,11	MCF-7	breast:
11	chr8:90730418..90730960-chr8:90860233..90861169,2	MCF-7	breast:
12	chr8:90730098..90733347-chr8:90733512..90737608,4	MCF-7	breast:
13	chr8:90730473..90731451-chr8:90996501..90997250,3	K562	blood:
14	chr8:90727118..90729538-chr8:90730165..90731877,3	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NBN-1	chr8:90729627-90733428	ENSG00000251136

No data

Variant related genes	Relation type
ENSG00000104320	Chromatin interaction
ENSG00000164823	Chromatin interaction
ENSG00000251136	Chromatin interaction
ENSG00000104325	Chromatin interaction
ENSG00000104312	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1003843	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10095743	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10112852	0.96[CEU][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12545569	0.84[EUR][1000 genomes]
rs12675281	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13252013	0.88[EUR][1000 genomes]
rs13252917	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13259882	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13279023	0.88[EUR][1000 genomes]
rs1397308	0.84[CEU][hapmap]
rs1605996	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1605997	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs184302	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs218893	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs218895	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs218899	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs218901	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]
rs218902	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[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]
rs218903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs218905	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs218907	0.96[CEU][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs218908	0.96[CEU][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs218909	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs218913	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs218914	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs218916	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs218925	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs218929	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs218932	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs218934	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs218936	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs218944	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs218946	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs218947	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs218948	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs218953	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2644021	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2644033	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2735870	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2735871	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2735873	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2735878	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2735882	0.81[AMR][1000 genomes]
rs2935115	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs385524	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs39499	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs39500	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs39503	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs39504	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs39505	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs39506	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs39509	0.81[AMR][1000 genomes]
rs39761	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs400411	0.81[AMR][1000 genomes]
rs40246	0.87[EUR][1000 genomes]
rs402886	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs40452	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs40453	0.81[AMR][1000 genomes]
rs40544	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs40545	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs405734	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs416324	0.81[AMR][1000 genomes]
rs419754	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs42490	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs431264	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs43134	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs43225	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs447618	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs454441	0.87[EUR][1000 genomes]
rs4961154	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4961155	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4961158	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56291556	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6470366	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6992985	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6993133	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7017316	0.81[ASN][1000 genomes]
rs7018416	0.80[CHB][hapmap]
rs7824932	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv831389	chr8:90575517-90753120	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv1031578	chr8:90670102-90757821	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv891180	chr8:90697810-90802491	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
5	nsv6294	chr8:90705780-90750101	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs218900	RP11-37B2.1	cis	Skin Sun Exposed Lower leg	GTEx
rs218900	RP11-37B2.1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90710200-90731200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr8:90710200-90736200	Weak transcription	Adipose Nuclei	Adipose
3	chr8:90711200-90733800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr8:90713200-90741200	Weak transcription	Left Ventricle	heart
5	chr8:90713400-90738000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr8:90713600-90756200	Weak transcription	Pancreas	Pancrea
7	chr8:90714200-90741400	Weak transcription	Right Ventricle	heart
8	chr8:90714400-90741000	Weak transcription	Gastric	stomach
9	chr8:90714800-90733000	Weak transcription	Placenta	Placenta
10	chr8:90715400-90741200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr8:90716800-90738000	Weak transcription	Brain Hippocampus Middle	brain
12	chr8:90717200-90733400	Weak transcription	Fetal Muscle Leg	muscle
13	chr8:90717200-90741000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr8:90717400-90738000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr8:90717600-90733400	Weak transcription	Aorta	Aorta
16	chr8:90717600-90733800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr8:90717800-90731200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr8:90717800-90736200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr8:90717800-90737800	Weak transcription	NHEK	skin
20	chr8:90717800-90738000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr8:90717800-90738000	Weak transcription	NH-A	brain
22	chr8:90717800-90747800	Weak transcription	Ovary	ovary
23	chr8:90718200-90731000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr8:90720800-90736000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr8:90720800-90742400	Weak transcription	Fetal Lung	lung
26	chr8:90721000-90740000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr8:90721200-90736400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr8:90721400-90731000	Weak transcription	Fetal Intestine Small	intestine
29	chr8:90721400-90735600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr8:90721400-90740400	Weak transcription	Fetal Intestine Large	intestine
31	chr8:90721800-90733400	Weak transcription	Fetal Stomach	stomach
32	chr8:90721800-90738400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr8:90724000-90731000	Weak transcription	NHDF-Ad	bronchial
34	chr8:90725200-90736200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr8:90725200-90740400	Weak transcription	Small Intestine	intestine
36	chr8:90725600-90731200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr8:90726600-90741400	Weak transcription	Esophagus	oesophagus
38	chr8:90726800-90738200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr8:90728400-90738000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr8:90729000-90731800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr8:90729200-90731000	Enhancers	K562	blood
42	chr8:90729200-90737800	Weak transcription	Fetal Heart	heart
43	chr8:90729400-90733600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr8:90729400-90733800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr8:90729600-90733800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr8:90729800-90731200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr8:90730000-90732200	Enhancers	HSMMtube	muscle
48	chr8:90730000-90733600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr8:90730000-90733600	Enhancers	Osteobl	bone
50	chr8:90730200-90731000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links