Variant report

Variant	rs2622711
Chromosome Location	chr3:137800656-137800657
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-A4GNT-3	chr3:137800576-137800671	NONHSAT092319

Extended variants
information (count: 118 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1107422	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11719358	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13100360	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1351446	0.87[ASN][1000 genomes]
rs1444577	0.84[ASN][1000 genomes]
rs1444578	0.82[ASN][1000 genomes]
rs1545816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1564496	0.84[ASN][1000 genomes]
rs17838821	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs179282	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2170309	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2246945	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2589259	0.84[ASN][1000 genomes]
rs2622697	0.84[ASN][1000 genomes]
rs2622698	0.87[ASN][1000 genomes]
rs2622704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2622705	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2622706	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2622707	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2622709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2622710	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2622713	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2622714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2622715	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2622716	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2622717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2622718	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2622719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2622720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2622724	0.88[ASN][1000 genomes]
rs2622725	0.88[ASN][1000 genomes]
rs2622726	0.88[ASN][1000 genomes]
rs2622727	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2622728	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2622729	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2622730	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2622746	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2724679	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2724687	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2724693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2724694	0.96[ASN][1000 genomes]
rs2724695	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2724697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2724698	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2724699	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2724700	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2724701	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2724702	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2724703	0.93[ASN][1000 genomes]
rs2724704	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2724705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2724706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2724707	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2724708	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2724713	0.88[ASN][1000 genomes]
rs2724716	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2724717	0.93[ASN][1000 genomes]
rs2724720	0.88[ASN][1000 genomes]
rs2724721	0.88[ASN][1000 genomes]
rs2724722	0.88[ASN][1000 genomes]
rs2724723	0.88[ASN][1000 genomes]
rs2724729	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28480035	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs329381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs329382	0.87[ASN][1000 genomes]
rs329383	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs329384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs329385	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs329388	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs329389	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs329390	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs329391	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs365504	0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs367439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs374045	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs382629	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs384828	1.00[CEU][hapmap];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];0.99[ASN][1000 genomes]
rs389697	0.91[ASN][1000 genomes]
rs390729	0.93[ASN][1000 genomes]
rs405265	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs405517	0.88[ASN][1000 genomes]
rs405602	1.00[CEU][hapmap];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];0.99[ASN][1000 genomes]
rs407009	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs419075	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs425938	0.93[ASN][1000 genomes]
rs436145	0.88[ASN][1000 genomes]
rs442800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs445025	0.93[ASN][1000 genomes]
rs446644	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs452195	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs453023	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4678403	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs618553	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6809258	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7613955	0.93[ASN][1000 genomes]
rs7629243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7639197	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs899983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9812778	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9814877	0.88[ASN][1000 genomes]
rs9834462	0.89[ASN][1000 genomes]
rs9834670	0.88[ASN][1000 genomes]
rs9842648	0.88[ASN][1000 genomes]
rs9842918	0.86[ASN][1000 genomes]
rs9857908	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9860229	0.89[ASN][1000 genomes]
rs9860630	0.86[ASN][1000 genomes]
rs9874211	0.81[ASN][1000 genomes]
rs996432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2757890	chr3:137611789-137933835	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2759180	chr3:137611789-137933835	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2751978	chr3:137715302-137890750	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1007857	chr3:137767454-137843106	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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
6	nsv1008563	chr3:137776151-137801394	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1002136	chr3:137776151-137806500	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv519971	chr3:137782655-137801213	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv522591	chr3:137782655-137801213	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137780000-137813400	Weak transcription	HUVEC	blood vessel
2	chr3:137780600-137811600	Weak transcription	Psoas Muscle	Psoas
3	chr3:137781000-137833200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:137783000-137802000	Weak transcription	Fetal Brain Female	brain
5	chr3:137783200-137811600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:137783200-137821200	Weak transcription	Colonic Mucosa	Colon
7	chr3:137785000-137801000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:137785400-137805600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:137786000-137802000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:137787600-137806600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:137787800-137802600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:137787800-137805200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr3:137789800-137803200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:137789800-137803600	Strong transcription	Fetal Lung	lung
15	chr3:137790800-137802400	Weak transcription	Fetal Intestine Large	intestine
16	chr3:137790800-137802800	Weak transcription	Brain Germinal Matrix	brain
17	chr3:137792000-137802000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:137792000-137802800	Weak transcription	Liver	Liver
19	chr3:137792000-137820600	Weak transcription	Esophagus	oesophagus
20	chr3:137792200-137805200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:137792400-137818200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:137792600-137802000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:137793600-137801400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:137793800-137803600	Strong transcription	Fetal Muscle Trunk	muscle
25	chr3:137794200-137801200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:137794600-137803400	Strong transcription	Fetal Muscle Leg	muscle
27	chr3:137794600-137803400	Strong transcription	Fetal Stomach	stomach
28	chr3:137795000-137801200	Strong transcription	Stomach Smooth Muscle	stomach
29	chr3:137795800-137803400	Strong transcription	Aorta	Aorta
30	chr3:137796200-137801600	Weak transcription	Fetal Kidney	kidney
31	chr3:137796200-137801800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:137796200-137802400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:137796200-137803800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:137796200-137811400	Weak transcription	Fetal Brain Male	brain
35	chr3:137796400-137802800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:137796600-137800800	Weak transcription	Spleen	Spleen
37	chr3:137796600-137800800	Genic enhancers	NHLF	lung
38	chr3:137796600-137803800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:137796800-137802200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:137796800-137802400	Genic enhancers	HSMM	muscle
41	chr3:137796800-137805200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:137797400-137802200	Weak transcription	Fetal Intestine Small	intestine
43	chr3:137797600-137802400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:137798000-137802000	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:137798200-137801200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr3:137798400-137801000	Enhancers	A549	lung
47	chr3:137798400-137801400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:137798400-137803200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:137798600-137803400	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:137798800-137803200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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