Variant report

Variant	rs2402923
Chromosome Location	chr7:128281256-128281257
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM71F2-1	chr7:128280776-128281433	NONHSAT123218
2	lnc-FAM71F2-1	chr7:128280784-128281433	NONHSAT123219
3	lnc-FAM71F2-1	chr7:128278644-128281373	NONHSAT123217

Extended variants
information (count: 140 )
Associated
traits (count: 46 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs1003241	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs10085580	0.81[ASN][1000 genomes]
rs10215560	0.84[ASN][1000 genomes]
rs10215566	0.84[ASN][1000 genomes]
rs10215947	0.84[ASN][1000 genomes]
rs10225988	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10227728	0.89[ASN][1000 genomes]
rs10229874	0.84[ASN][1000 genomes]
rs10237278	0.84[ASN][1000 genomes]
rs10237880	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10276417	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10954192	0.80[ASN][1000 genomes]
rs10954193	0.87[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs10954194	0.80[ASN][1000 genomes]
rs10954195	0.80[ASN][1000 genomes]
rs1109552	0.87[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs11769769	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs11978608	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11979586	0.85[ASN][1000 genomes]
rs12667202	0.80[ASN][1000 genomes]
rs12670271	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs12670823	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12671767	0.80[ASN][1000 genomes]
rs12672443	0.82[ASN][1000 genomes]
rs12672576	0.80[ASN][1000 genomes]
rs12673060	0.82[ASN][1000 genomes]
rs12673998	0.88[ASN][1000 genomes]
rs12674125	0.87[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs12706856	0.83[ASN][1000 genomes]
rs12706857	0.84[ASN][1000 genomes]
rs13438170	0.84[ASN][1000 genomes]
rs1450874	0.87[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs17169024	0.87[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs17169357	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1809082	0.87[ASN][1000 genomes]
rs1970827	0.85[ASN][1000 genomes]
rs1970828	0.86[ASN][1000 genomes]
rs2044834	0.86[ASN][1000 genomes]
rs2290229	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs2402907	0.88[ASN][1000 genomes]
rs2443110	0.82[ASN][1000 genomes]
rs28505422	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34614236	0.88[ASN][1000 genomes]
rs35394926	0.87[ASN][1000 genomes]
rs3857849	0.87[ASN][1000 genomes]
rs3896308	0.84[ASN][1000 genomes]
rs3927852	0.85[ASN][1000 genomes]
rs3931943	0.86[ASN][1000 genomes]
rs4079001	0.86[ASN][1000 genomes]
rs4079003	0.87[ASN][1000 genomes]
rs4260830	0.83[ASN][1000 genomes]
rs4554406	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs4562239	0.82[ASN][1000 genomes]
rs4579449	0.82[ASN][1000 genomes]
rs4728128	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs4728130	0.87[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs4731480	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4731482	0.82[ASN][1000 genomes]
rs4731484	0.87[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4731486	0.84[ASN][1000 genomes]
rs4731488	0.87[ASN][1000 genomes]
rs4731492	0.80[ASN][1000 genomes]
rs4731493	0.80[ASN][1000 genomes]
rs4731494	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4731503	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs55860694	0.82[ASN][1000 genomes]
rs55982013	0.82[ASN][1000 genomes]
rs56033435	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56052829	0.83[ASN][1000 genomes]
rs56111366	0.82[ASN][1000 genomes]
rs56189614	0.83[ASN][1000 genomes]
rs56278047	0.83[ASN][1000 genomes]
rs56946745	0.88[ASN][1000 genomes]
rs57226192	0.82[ASN][1000 genomes]
rs57370656	0.88[ASN][1000 genomes]
rs58133562	0.82[ASN][1000 genomes]
rs59066415	0.82[ASN][1000 genomes]
rs59154282	0.83[ASN][1000 genomes]
rs59594227	0.82[ASN][1000 genomes]
rs60515997	0.82[ASN][1000 genomes]
rs61146845	0.82[ASN][1000 genomes]
rs61318942	0.80[ASN][1000 genomes]
rs62479751	0.83[ASN][1000 genomes]
rs62479756	0.83[ASN][1000 genomes]
rs62479757	0.83[ASN][1000 genomes]
rs62481868	0.85[ASN][1000 genomes]
rs62481869	0.86[ASN][1000 genomes]
rs62481873	0.83[ASN][1000 genomes]
rs62481883	0.86[ASN][1000 genomes]
rs62481890	0.88[ASN][1000 genomes]
rs62481892	0.88[ASN][1000 genomes]
rs62481895	0.88[ASN][1000 genomes]
rs62481896	0.81[ASN][1000 genomes]
rs62481897	0.88[ASN][1000 genomes]
rs62481901	0.87[ASN][1000 genomes]
rs62481906	0.86[ASN][1000 genomes]
rs62481923	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs62483297	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62483302	0.80[ASN][1000 genomes]
rs62483305	0.82[ASN][1000 genomes]
rs62483348	0.81[ASN][1000 genomes]
rs6467185	0.83[ASN][1000 genomes]
rs6467186	0.83[ASN][1000 genomes]
rs6467188	0.84[ASN][1000 genomes]
rs6467189	0.84[ASN][1000 genomes]
rs6467194	0.83[ASN][1000 genomes]
rs6467195	0.83[ASN][1000 genomes]
rs6467196	0.81[ASN][1000 genomes]
rs6467197	0.81[ASN][1000 genomes]
rs6467202	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6467203	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6467210	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs6945126	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6955960	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6958788	0.87[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs6969554	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs6974153	0.82[ASN][1000 genomes]
rs6975194	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6978360	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6978887	0.80[ASN][1000 genomes]
rs6979304	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6979575	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs73233862	0.82[ASN][1000 genomes]
rs7385007	0.83[ASN][1000 genomes]
rs7385676	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7792915	0.84[ASN][1000 genomes]
rs7793136	0.87[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs7795558	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7797359	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7797745	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs7802149	0.80[ASN][1000 genomes]
rs7802233	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7804825	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7807293	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9690564	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9768325	0.81[ASN][1000 genomes]
rs9770238	0.84[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	nsv427806	chr7:128179989-128428182	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv970938	chr7:128256300-128300276	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv981679	chr7:128278778-128282292	Weak transcription Strong transcription	lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:46)

SNP	Gene	Cis/trans	Tissue	Source
rs2402923	CICP14	cis	Skin Sun Exposed Lower leg	GTEx
rs2402923	RP11-274B21.1	cis	Esophagus Muscularis	GTEx
rs2402923	RP11-274B21.4	cis	Whole Blood	GTEx
rs2402923	RP11-274B21.4	cis	Stomach	GTEx
rs2402923	RP11-274B21.4	cis	lung	GTEx
rs2402923	RP11-274B21.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2402923	RP11-274B21.2	cis	Skin Sun Exposed Lower leg	GTEx
rs2402923	RP11-274B21.1	cis	Artery Tibial	GTEx
rs2402923	CPA4	cis	cerebellum	SCAN
rs2402923	CICP14	cis	Adipose Subcutaneous	GTEx
rs2402923	RP11-274B21.1	cis	lung	GTEx
rs2402923	RP11-274B21.4	cis	Adipose Subcutaneous	GTEx
rs2402923	RP11-274B21.4	cis	Thyroid	GTEx
rs2402923	RP11-274B21.2	cis	Adipose Subcutaneous	GTEx
rs2402923	RP11-274B21.1	cis	Whole Blood	GTEx
rs2402923	RP11-274B21.4	cis	Muscle Skeletal	GTEx
rs2402923	RP11-274B21.2	cis	Thyroid	GTEx
rs2402923	RP11-274B21.1	cis	Thyroid	GTEx
rs2402923	RP11-274B21.3	cis	lung	GTEx
rs2402923	RP11-274B21.4	cis	Artery Aorta	GTEx
rs2402923	CICP14	cis	Artery Tibial	GTEx
rs2402923	RP11-274B21.2	cis	Artery Tibial	GTEx
rs2402923	RP11-274B21.2	cis	Nerve Tibial	GTEx
rs2402923	RP11-274B21.4	cis	Artery Tibial	GTEx
rs2402923	RP11-274B21.1	cis	Artery Aorta	GTEx
rs2402923	RP11-274B21.3	cis	Adipose Subcutaneous	GTEx
rs2402923	RP11-274B21.2	cis	Muscle Skeletal	GTEx
rs2402923	RP11-274B21.4	cis	Skin Sun Exposed Lower leg	GTEx
rs2402923	RP11-274B21.1	cis	Muscle Skeletal	GTEx
rs2402923	CICP14	cis	Muscle Skeletal	GTEx
rs2402923	RP11-274B21.3	cis	Nerve Tibial	GTEx
rs2402923	RP11-274B21.3	cis	Muscle Skeletal	GTEx
rs2402923	RP11-274B21.2	cis	lung	GTEx
rs2402923	RP11-274B21.1	cis	Nerve Tibial	GTEx
rs2402923	RP11-274B21.1	cis	Adipose Subcutaneous	GTEx
rs2402923	CICP14	cis	lung	GTEx
rs2402923	RP11-274B21.4	cis	Esophagus Muscularis	GTEx
rs2402923	RP11-274B21.2	cis	Whole Blood	GTEx
rs2402923	RP11-274B21.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2402923	RP11-274B21.2	cis	Stomach	GTEx
rs2402923	METTL2B	cis	parietal	SCAN
rs2402923	RP11-274B21.4	cis	Esophagus Mucosa	GTEx
rs2402923	CICP14	cis	Thyroid	GTEx
rs2402923	RP11-274B21.4	cis	Nerve Tibial	GTEx
rs2402923	RP11-274B21.3	cis	Thyroid	GTEx
rs2402923	RP11-274B21.3	cis	Artery Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128237800-128290400	Weak transcription	HepG2	liver
2	chr7:128239200-128287200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr7:128239200-128296400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:128242600-128292800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:128246600-128284800	Weak transcription	Stomach Mucosa	stomach
6	chr7:128249600-128283200	Weak transcription	Hela-S3	cervix
7	chr7:128249600-128285800	Weak transcription	Fetal Heart	heart
8	chr7:128249600-128286800	Weak transcription	HSMMtube	muscle
9	chr7:128249600-128289000	Weak transcription	NHEK	skin
10	chr7:128249600-128293400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:128249600-128295200	Weak transcription	NH-A	brain
12	chr7:128249600-128297600	Weak transcription	HUVEC	blood vessel
13	chr7:128249600-128308400	Weak transcription	HSMM	muscle
14	chr7:128249600-128312200	Weak transcription	Psoas Muscle	Psoas
15	chr7:128249600-128319600	Weak transcription	NHLF	lung
16	chr7:128252200-128287600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr7:128256800-128288600	Weak transcription	Osteobl	bone
18	chr7:128258600-128287400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr7:128260000-128296400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr7:128260400-128300600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:128262200-128293200	Weak transcription	Brain Germinal Matrix	brain
22	chr7:128262600-128283800	Weak transcription	Small Intestine	intestine
23	chr7:128263000-128286600	Weak transcription	Fetal Brain Male	brain
24	chr7:128265800-128289000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr7:128266400-128290400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr7:128267200-128287400	Strong transcription	Fetal Muscle Leg	muscle
27	chr7:128272200-128300000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:128272400-128285800	Weak transcription	Fetal Kidney	kidney
29	chr7:128272400-128290400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr7:128272400-128290400	Weak transcription	K562	blood
31	chr7:128272400-128292400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr7:128272400-128293200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr7:128273600-128290600	Weak transcription	Fetal Brain Female	brain
34	chr7:128273800-128283600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr7:128273800-128291800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr7:128274200-128283800	Weak transcription	GM12878-XiMat	blood
37	chr7:128274200-128296400	Weak transcription	Colonic Mucosa	Colon
38	chr7:128274400-128283800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr7:128274400-128287400	Strong transcription	Liver	Liver
40	chr7:128274600-128291200	Weak transcription	Esophagus	oesophagus
41	chr7:128275600-128287400	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr7:128275600-128295000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr7:128275800-128282600	Strong transcription	Fetal Thymus	thymus
44	chr7:128275800-128289600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr7:128276000-128287200	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr7:128276000-128287600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr7:128276200-128284400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr7:128276200-128287400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr7:128277200-128281400	Strong transcription	Thymus	Thymus
50	chr7:128277200-128282400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links