Variant report

Variant	rs896248
Chromosome Location	chr2:100078475-100078476
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:100075556..100080404-chr2:100103648..100108163,7	K562	blood:
2	chr2:100077312..100079121-chr2:100100989..100102811,2	K562	blood:

Variant related genes	Relation type
ENSG00000135945	Chromatin interaction

Extended variants
information (count: 151 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs1000409	0.84[CHB][hapmap];0.88[ASN][1000 genomes]
rs1011633	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10170425	0.88[ASN][1000 genomes]
rs10172068	0.84[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs10172752	0.83[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs10173466	0.83[ASN][1000 genomes]
rs10187843	0.81[JPT][hapmap]
rs1053544	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10865031	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11123782	0.82[JPT][hapmap]
rs11123785	0.87[JPT][hapmap]
rs11123786	0.82[JPT][hapmap]
rs11683651	0.82[JPT][hapmap]
rs11686535	0.82[JPT][hapmap]
rs11687870	0.82[JPT][hapmap]
rs11884686	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11887109	0.85[ASN][1000 genomes]
rs11887574	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs11892441	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11899745	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11902994	0.82[JPT][hapmap]
rs12052986	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12233086	0.87[JPT][hapmap]
rs12233126	0.87[JPT][hapmap]
rs12464785	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12465846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12475639	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12623540	0.82[JPT][hapmap]
rs13014360	0.81[JPT][hapmap]
rs13017871	0.82[JPT][hapmap]
rs13018274	0.82[JPT][hapmap]
rs13026997	0.82[JPT][hapmap]
rs13392042	0.88[ASN][1000 genomes]
rs13394688	0.86[ASN][1000 genomes]
rs13427780	0.82[ASN][1000 genomes]
rs1451243	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs1451245	0.88[CHB][hapmap];0.87[JPT][hapmap]
rs1451246	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1584647	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1584648	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17022564	0.93[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17022629	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1839666	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1839667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1901283	0.88[ASN][1000 genomes]
rs1973011	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2053917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2122748	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242036	0.86[JPT][hapmap]
rs2290255	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2290256	0.82[JPT][hapmap]
rs2290257	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs2290261	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2309576	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2309585	0.84[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs2309604	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2309617	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28369943	0.88[ASN][1000 genomes]
rs28382892	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs28382946	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28382984	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3087386	0.83[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs3749087	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3791212	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3792134	0.84[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs3792135	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs3792136	0.83[CHB][hapmap]
rs3792137	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]
rs3792142	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3792144	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792146	0.83[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs3792149	0.84[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs3792152	0.88[CHB][hapmap]
rs3811555	0.82[JPT][hapmap]
rs3828316	0.82[JPT][hapmap]
rs4143760	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4476396	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535093	0.82[JPT][hapmap]
rs4850901	0.82[JPT][hapmap]
rs4851200	0.82[JPT][hapmap]
rs4851204	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4851205	0.82[JPT][hapmap]
rs4851206	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]
rs4851208	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4851209	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55815229	0.81[EUR][1000 genomes]
rs57242893	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs57977991	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58086269	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58958283	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59178618	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59661148	0.83[AMR][1000 genomes]
rs60257640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60335031	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61103312	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62153855	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62155809	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6542879	0.84[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs6542880	0.84[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs6542881	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6542882	0.84[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs6708861	0.82[JPT][hapmap]
rs6711073	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6713608	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6713792	0.84[ASN][1000 genomes]
rs6714244	0.83[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs6715321	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6717515	0.85[ASN][1000 genomes]
rs6720885	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6727483	0.87[JPT][hapmap]
rs6732750	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6737560	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6761390	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs717454	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7558062	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7560996	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7561079	0.82[JPT][hapmap]
rs7561616	0.82[JPT][hapmap]
rs7563455	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563462	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564587	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7567674	0.83[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs7571202	0.82[JPT][hapmap]
rs7572779	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7574135	0.82[JPT][hapmap]
rs7579403	0.82[JPT][hapmap]
rs7580448	0.84[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs7584127	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7585019	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]
rs7585721	0.82[JPT][hapmap]
rs7587419	0.82[JPT][hapmap]
rs7589365	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7593274	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7594838	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs7597045	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7597141	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7598629	0.88[ASN][1000 genomes]
rs7601470	0.82[JPT][hapmap]
rs7601730	0.82[JPT][hapmap]
rs7602923	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7606977	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs769105	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]
rs896249	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs959929	0.84[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs9941566	0.81[JPT][hapmap]

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	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1014604	chr2:99980851-100097884	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1006625	chr2:99984550-100096371	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv874700	chr2:100062163-100099989	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv535841	chr2:100072790-100112121	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs896248	LYG1	cis	Adipose Subcutaneous	GTEx
rs896248	LYG1	cis	Nerve Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100006000-100081200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr2:100034200-100088800	Weak transcription	Small Intestine	intestine
3	chr2:100041600-100083400	Weak transcription	Brain Substantia Nigra	brain
4	chr2:100048200-100090600	Weak transcription	Stomach Mucosa	stomach
5	chr2:100055400-100083200	Weak transcription	Right Ventricle	heart
6	chr2:100055600-100079800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:100055800-100089000	Weak transcription	Pancreas	Pancrea
8	chr2:100055800-100092600	Weak transcription	Gastric	stomach
9	chr2:100056600-100091000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:100060400-100079200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr2:100061800-100079200	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr2:100061800-100079400	Strong transcription	Liver	Liver
13	chr2:100062200-100079000	Strong transcription	Primary B cells from peripheral blood	blood
14	chr2:100062200-100080600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:100062200-100080600	Strong transcription	HepG2	liver
16	chr2:100062400-100079200	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr2:100062600-100079200	Strong transcription	Duodenum Mucosa	Duodenum
18	chr2:100063400-100078800	Strong transcription	Adipose Nuclei	Adipose
19	chr2:100063400-100079200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr2:100064000-100078800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr2:100065400-100078600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:100065400-100087400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:100067200-100079200	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:100067400-100081400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:100067600-100079200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:100067800-100080000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:100068000-100079200	Strong transcription	Fetal Muscle Leg	muscle
28	chr2:100070200-100079000	Strong transcription	Osteobl	bone
29	chr2:100070600-100078800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:100070600-100079200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:100070800-100078800	Strong transcription	Primary B cells from cord blood	blood
32	chr2:100071000-100079200	Strong transcription	NHEK	skin
33	chr2:100071200-100079200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:100071200-100080600	Strong transcription	Dnd41	blood
35	chr2:100071400-100080400	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr2:100071600-100079400	Strong transcription	Primary T cells from cord blood	blood
37	chr2:100071600-100080400	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr2:100071800-100079000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr2:100072000-100079200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:100072400-100078600	Strong transcription	HMEC	breast
41	chr2:100072400-100078800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:100072600-100079200	Strong transcription	HSMM	muscle
43	chr2:100073200-100078600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:100073400-100090000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr2:100074200-100084800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr2:100075000-100078800	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:100075200-100080400	Strong transcription	Fetal Intestine Large	intestine
48	chr2:100075200-100090400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr2:100075200-100103000	Weak transcription	Hela-S3	cervix
50	chr2:100075400-100078800	Strong transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links