Variant report

Variant	rs4527246
Chromosome Location	chr2:96560303-96560304
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1043092	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11164053	0.87[EUR][1000 genomes]
rs11683523	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs11687113	0.82[CEU][hapmap]
rs11689832	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11695514	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs12464148	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2315417	0.87[AMR][1000 genomes]
rs2315421	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2438972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2438978	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs2462774	0.83[CEU][hapmap]
rs2579519	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs2692893	0.86[CEU][hapmap]
rs28856333	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34233881	0.86[ASN][1000 genomes]
rs34639392	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4063021	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4332959	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4907224	0.80[EUR][1000 genomes]
rs4907288	0.83[CEU][hapmap]
rs56791141	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60273147	0.84[EUR][1000 genomes]
rs61409777	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62153670	0.80[EUR][1000 genomes]
rs62153678	0.87[EUR][1000 genomes]
rs62153679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62153692	0.85[EUR][1000 genomes]
rs62153700	0.81[EUR][1000 genomes]
rs62156932	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6706905	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6707583	0.85[AMR][1000 genomes]
rs6717101	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6719831	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6740563	0.82[CEU][hapmap]
rs7597765	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3416818	chr2:96072529-96680708	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv874660	chr2:96091132-96669134	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv516044	chr2:96150959-96683378	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1003371	chr2:96326106-96684876	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv874662	chr2:96334397-96578621	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv874665	chr2:96370571-96596515	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv874666	chr2:96370571-96691125	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv1004482	chr2:96408987-96596717	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Bivalent Enhancer	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv428054	chr2:96438238-96627125	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv961832	chr2:96453677-96671971	Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv874667	chr2:96465201-96596515	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv874668	chr2:96465201-96600569	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
13	esv1826589	chr2:96468292-96583910	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
14	esv1826305	chr2:96468492-96583710	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
15	esv1848259	chr2:96477989-96583252	ZNF genes & repeats Strong transcription Enhancers Weak transcription Genic enhancers	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv834304	chr2:96493545-96667472	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv10093	chr2:96524159-96583335	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
18	esv1847850	chr2:96532929-96582175	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv508154	chr2:96534336-96609925	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
20	esv1849015	chr2:96534572-96581975	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv1004486	chr2:96544604-96684876	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
22	esv1847704	chr2:96545150-96583452	Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
23	esv3506800	chr2:96545563-96588565	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
24	esv3506801	chr2:96545563-96588565	Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
25	nsv874669	chr2:96547820-96691125	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
26	esv1010947	chr2:96549314-96586310	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
27	esv1797061	chr2:96550572-96582175	Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
28	esv1793058	chr2:96553765-96583121	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
29	nsv818073	chr2:96554851-96683378	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
30	esv1795949	chr2:96554897-96583452	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
31	esv1825688	chr2:96555097-96583710	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
32	esv16343	chr2:96556623-96579733	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
33	nsv961623	chr2:96557042-96560529	Weak transcription Strong transcription Enhancers Genic enhancers	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4527246	GPAT2	cis	Muscle Skeletal	GTEx
rs4527246	FAHD2CP	cis	lung	GTEx
rs4527246	FAHD2CP	cis	Muscle Skeletal	GTEx
rs4527246	FAHD2CP	cis	Adipose Subcutaneous	GTEx
rs4527246	ASTL	cis	Esophagus Mucosa	GTEx
rs4527246	ADRA2B	cis	Thyroid	GTEx
rs4527246	ADRA2B	cis	Nerve Tibial	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96502600-96561400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:96502800-96585000	Weak transcription	Left Ventricle	heart
3	chr2:96502800-96616600	Weak transcription	Fetal Stomach	stomach
4	chr2:96503000-96563600	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:96506600-96562000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:96536000-96576800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:96541000-96582000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:96541000-96595400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:96541600-96595200	Weak transcription	Fetal Brain Male	brain
10	chr2:96543800-96596200	Weak transcription	K562	blood
11	chr2:96544600-96561800	Weak transcription	Colon Smooth Muscle	Colon
12	chr2:96545000-96576400	Weak transcription	Brain Germinal Matrix	brain
13	chr2:96546000-96577400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:96546800-96562200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr2:96547000-96586400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:96547600-96575800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:96548000-96563000	Weak transcription	Right Ventricle	heart
18	chr2:96548200-96564200	Weak transcription	A549	lung
19	chr2:96549600-96563000	Weak transcription	Liver	Liver
20	chr2:96549800-96576400	Weak transcription	Thymus	Thymus
21	chr2:96549800-96576600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr2:96549800-96579600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:96549800-96580200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr2:96549800-96588600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:96549800-96590600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:96550000-96562000	Weak transcription	Placenta	Placenta
27	chr2:96551400-96600800	Weak transcription	Brain Angular Gyrus	brain
28	chr2:96551800-96588600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr2:96552400-96576200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:96552400-96595400	Weak transcription	Fetal Kidney	kidney
31	chr2:96554000-96580400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:96554200-96588600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr2:96556000-96576400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr2:96556000-96583800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr2:96556200-96561600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:96556200-96562000	Weak transcription	HSMM	muscle
37	chr2:96556200-96562400	Weak transcription	NH-A	brain
38	chr2:96556200-96576800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:96556200-96577400	Weak transcription	Fetal Muscle Leg	muscle
40	chr2:96556200-96582000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:96556200-96582400	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr2:96556200-96583000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr2:96556200-96645000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr2:96556400-96561600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:96556400-96576400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr2:96556400-96577200	Weak transcription	Primary T cells from cord blood	blood
47	chr2:96556400-96577600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:96556400-96578000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr2:96556400-96579800	Weak transcription	Fetal Brain Female	brain
50	chr2:96556400-96582200	Weak transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links