Variant report

Variant	rs4854249
Chromosome Location	chr2:95930630-95930631
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	chr2:95930484..95933325-chr2:95937443..95939071,2	K562	blood:
2	chr2:95930484..95933439-chr2:95936621..95939071,2	K562	blood:

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10195614	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1104775	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11164122	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs11897976	0.90[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs12992066	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1559483	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs17119148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes]
rs1862897	0.90[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs1875402	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1966272	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2001254	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2010533	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2042477	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs2098768	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2113417	0.90[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs2320339	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2320619	0.81[EUR][1000 genomes]
rs2320620	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs2320621	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2320624	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3105100	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3105101	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs3105102	0.91[EUR][1000 genomes]
rs3105104	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3105105	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3112221	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3112222	0.84[EUR][1000 genomes]
rs3112223	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3112225	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3112228	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3112229	0.85[CEU][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3112230	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3112231	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3112984	0.82[EUR][1000 genomes]
rs3112985	0.80[EUR][1000 genomes]
rs3112986	0.82[EUR][1000 genomes]
rs3112987	0.82[EUR][1000 genomes]
rs3112995	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3112996	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3112997	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3112999	0.91[EUR][1000 genomes]
rs3113000	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3113001	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3755519	0.83[EUR][1000 genomes]
rs3755520	0.86[CEU][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs3755521	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs3755523	0.86[CEU][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs3755525	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs3772031	0.90[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs3772032	0.90[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs3772033	0.90[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs3772037	0.83[EUR][1000 genomes]
rs3772041	0.86[CEU][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs3772042	0.86[CEU][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs3772043	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs3772044	0.95[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs3821341	0.81[CEU][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs4283455	0.83[EUR][1000 genomes]
rs4854243	0.82[EUR][1000 genomes]
rs4854247	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6577012	0.86[CEU][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs6577013	0.86[CEU][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs6715813	0.86[CEU][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs6719098	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6725821	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6741001	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs6750542	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs7574862	0.86[CEU][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs7580685	0.86[CEU][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs7585473	0.83[EUR][1000 genomes]
rs7585914	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7586229	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7594144	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs7602807	0.83[EUR][1000 genomes]
rs870393	0.81[CEU][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs889851	0.86[CEU][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs889852	0.86[CEU][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs889853	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs918811	0.90[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs9678800	0.90[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs9989786	0.85[CEU][hapmap];0.94[TSI][hapmap];0.84[EUR][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	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv1008945	chr2:95745367-96062107	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv817299	chr2:95799814-96159275	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1007627	chr2:95878031-95973743	Enhancers ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv535822	chr2:95878031-95973743	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv998370	chr2:95897299-96074071	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv535823	chr2:95897299-96074071	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv998014	chr2:95913278-96296630	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4854249	SRA1	trans	parietal	SCAN
rs4854249	KCNIP3	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95924000-95941200	Weak transcription	Right Ventricle	heart
2	chr2:95924400-95941400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr2:95925400-95933200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:95925600-95953800	Weak transcription	Right Atrium	heart
5	chr2:95925800-95934000	Weak transcription	Spleen	Spleen
6	chr2:95926800-95933400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:95926800-95939400	Weak transcription	Esophagus	oesophagus
8	chr2:95926800-95953600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr2:95930000-95931400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr2:95930000-95932400	Enhancers	Brain Hippocampus Middle	brain
11	chr2:95930000-95956200	Weak transcription	Fetal Brain Female	brain
12	chr2:95930200-95931400	Enhancers	Brain Anterior Caudate	brain
13	chr2:95930200-95931400	Enhancers	Brain Cingulate Gyrus	brain
14	chr2:95930200-95931400	Enhancers	Brain Substantia Nigra	brain
15	chr2:95930400-95931200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:95930400-95931600	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr2:95930600-95931000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr2:95930600-95931200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:95930600-95931200	Enhancers	Fetal Muscle Leg	muscle
20	chr2:95930600-95931200	Enhancers	Fetal Stomach	stomach
21	chr2:95930600-95931400	Enhancers	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links