Variant report

Variant	rs56388246
Chromosome Location	chr7:69781930-69781931
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WBSCR17-5	chr7:69781902-69782032	NONHSAT121328

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10081305	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10085908	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10156142	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10227424	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10228786	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10234106	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10234121	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10238049	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10248401	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10248606	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10251433	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10254871	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10256093	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10262102	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10266802	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10276912	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10281537	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11762035	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11764141	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11764397	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11764782	0.87[EUR][1000 genomes]
rs11766424	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11768151	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11770380	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11770466	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11770695	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11770963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11773411	0.81[AMR][1000 genomes]
rs12112891	0.81[AMR][1000 genomes]
rs12113743	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13437638	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17141168	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17141181	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17141191	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17141193	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28433534	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28464032	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28489338	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28582872	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28617759	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28657792	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2866276	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34944443	0.81[AMR][1000 genomes]
rs35862187	0.84[EUR][1000 genomes]
rs4364526	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4557583	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55946510	0.81[AMR][1000 genomes]
rs56063609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56376205	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56410838	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56669413	0.81[AMR][1000 genomes]
rs56999082	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57370717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58873380	0.85[ASN][1000 genomes]
rs60847182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6944701	0.91[EUR][1000 genomes]
rs6948174	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6950849	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6967512	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6976263	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73160193	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73171731	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73173531	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73173550	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73173577	0.81[AMR][1000 genomes]
rs73173581	0.81[AMR][1000 genomes]
rs73173583	0.81[AMR][1000 genomes]
rs7780665	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7796273	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7798890	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7805165	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018749	chr7:69149029-69995112	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv532782	chr7:69383651-70189959	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv916345	chr7:69520612-69784809	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv869342	chr7:69671501-69958576	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv607431	chr7:69699074-69828729	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv888337	chr7:69707076-69952187	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv529669	chr7:69709373-69974708	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1028870	chr7:69742438-69879231	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69776000-69786600	Enhancers	Primary T cells from cord blood	blood
2	chr7:69776600-69782000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr7:69778200-69782000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:69778200-69782600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr7:69778600-69789600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr7:69778800-69782800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr7:69779000-69783400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr7:69779000-69783600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr7:69779000-69784000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr7:69779200-69783600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr7:69779200-69783800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr7:69779200-69784400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr7:69779400-69783400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr7:69779400-69783800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr7:69779400-69783800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr7:69779600-69802200	Weak transcription	Primary B cells from cord blood	blood
17	chr7:69780800-69785800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:69781200-69784400	Enhancers	Primary T cells fromperipheralblood	blood
19	chr7:69781400-69782400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr7:69781600-69782600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr7:69781600-69783800	Enhancers	Lung	lung
22	chr7:69781600-69784000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr7:69781600-69784800	Enhancers	Dnd41	blood
24	chr7:69781800-69782000	Enhancers	Left Ventricle	heart
25	chr7:69781800-69782000	Enhancers	Right Ventricle	heart
26	chr7:69781800-69782200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr7:69781800-69782200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr7:69781800-69782200	Enhancers	Gastric	stomach
29	chr7:69781800-69782800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr7:69781800-69782800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr7:69781800-69782800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr7:69781800-69782800	Enhancers	Aorta	Aorta
33	chr7:69781800-69782800	Enhancers	NH-A	brain
34	chr7:69781800-69782800	Flanking Active TSS	NHEK	skin
35	chr7:69781800-69783000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr7:69781800-69783000	Enhancers	HMEC	breast
37	chr7:69781800-69783400	Enhancers	Pancreas	Pancrea
38	chr7:69781800-69783600	Enhancers	Rectal Smooth Muscle	rectum
39	chr7:69781800-69783800	Enhancers	Esophagus	oesophagus
40	chr7:69781800-69784000	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr7:69781800-69784400	Enhancers	Fetal Thymus	thymus

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