Variant report

Variant	rs7035964
Chromosome Location	chr9:94793445-94793446
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CENPP-13	chr9:94793430-94794193	NONHSAT133148

Extended variants
information (count: 127 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10115181	0.86[ASN][1000 genomes]
rs10115565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10116088	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10117113	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10117143	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10117394	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10118409	0.87[AMR][1000 genomes]
rs10118614	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10118847	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10119603	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10119983	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10121430	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10121694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10121928	0.93[AMR][1000 genomes]
rs10122415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10122798	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10123181	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10123678	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10124473	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10124705	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs10992194	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10992202	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10992223	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12336291	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12336497	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12336689	0.97[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12338124	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12341602	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12341791	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12343645	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12343647	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12344414	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12345896	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12347966	0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12348496	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12349001	0.82[AMR][1000 genomes]
rs12349327	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12352341	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12353142	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12353321	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16908106	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs16908113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16908131	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28391324	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28429191	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28437390	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28477960	0.93[AMR][1000 genomes]
rs28504279	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28505748	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs28513744	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28552704	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28637477	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28735483	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28744634	0.98[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28759240	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28804693	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs28819206	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28825409	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28883017	0.86[ASN][1000 genomes]
rs3858086	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4302907	0.86[ASN][1000 genomes]
rs4344138	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4498616	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4560856	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4604504	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56204501	1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs56208357	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs56248784	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs56266486	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs57496363	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57862149	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs58224960	0.96[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs58679317	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59790820	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60230478	0.99[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60743157	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61000917	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61246786	0.89[AFR][1000 genomes]
rs61456615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61596207	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6479397	0.81[ASN][1000 genomes]
rs7018595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7018827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7021285	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7021293	0.81[ASN][1000 genomes]
rs7021408	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7024215	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7025703	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7027257	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7028378	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7033888	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7034509	0.91[ASN][1000 genomes]
rs7039366	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7045602	1.00[AMR][1000 genomes]
rs7046206	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7047389	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73510406	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs73510411	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs73512337	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs73512339	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73512378	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73522907	0.93[AMR][1000 genomes]
rs73522929	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs73527329	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs73527330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73653014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7848959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7849664	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7851249	0.81[ASN][1000 genomes]
rs7851412	0.93[AMR][1000 genomes]
rs7852989	0.86[ASN][1000 genomes]
rs7856188	0.89[AFR][1000 genomes]
rs7864340	0.86[ASN][1000 genomes]
rs7865994	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7867659	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7870339	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7870565	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7871565	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7871997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7872238	0.91[ASN][1000 genomes]
rs9696251	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9697261	0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv831653	chr9:94692454-94867542	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7035964	SPTLC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94779000-94794600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:94781200-94794600	Weak transcription	Fetal Stomach	stomach
3	chr9:94782200-94794600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:94782400-94795600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr9:94785200-94795200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr9:94785400-94794200	Weak transcription	NHEK	skin
7	chr9:94785400-94795200	Weak transcription	HMEC	breast
8	chr9:94786200-94794600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr9:94787200-94794600	Weak transcription	Thymus	Thymus
10	chr9:94787200-94794600	Weak transcription	HSMMtube	muscle
11	chr9:94787400-94795000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr9:94788200-94794200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:94788400-94794200	Weak transcription	Osteobl	bone
14	chr9:94788400-94794600	Weak transcription	Fetal Intestine Small	intestine
15	chr9:94788400-94795800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr9:94788600-94794000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr9:94788800-94794600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr9:94788800-94794600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr9:94788800-94795400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:94789000-94794600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:94789000-94794600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:94789000-94795200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr9:94789200-94794600	Weak transcription	Primary T cells from cord blood	blood
24	chr9:94789200-94794600	Weak transcription	Esophagus	oesophagus
25	chr9:94789200-94794600	Weak transcription	Spleen	Spleen
26	chr9:94789400-94793800	Weak transcription	Placenta	Placenta
27	chr9:94789400-94794600	Weak transcription	Fetal Muscle Leg	muscle
28	chr9:94789800-94794200	Weak transcription	Colon Smooth Muscle	Colon
29	chr9:94789800-94794600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr9:94790000-94794000	Weak transcription	Fetal Kidney	kidney
31	chr9:94790000-94794400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr9:94790000-94796400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr9:94790200-94794600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:94790400-94794600	Weak transcription	Aorta	Aorta
35	chr9:94790400-94794600	Weak transcription	Ovary	ovary
36	chr9:94790600-94793600	Weak transcription	Adipose Nuclei	Adipose
37	chr9:94790600-94794000	Weak transcription	HSMM	muscle
38	chr9:94790800-94793600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr9:94790800-94793600	Weak transcription	Brain Substantia Nigra	brain
40	chr9:94790800-94794000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr9:94790800-94794600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr9:94790800-94794600	Weak transcription	NH-A	brain
43	chr9:94790800-94795200	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr9:94791000-94794400	Weak transcription	NHLF	lung
45	chr9:94791000-94794600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr9:94791000-94794600	Weak transcription	Left Ventricle	heart
47	chr9:94791000-94795400	Weak transcription	A549	lung
48	chr9:94791000-94795800	Weak transcription	Colonic Mucosa	Colon
49	chr9:94791200-94793800	Weak transcription	Fetal Muscle Trunk	muscle
50	chr9:94791200-94794200	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links