Variant report

Variant	rs11978288
Chromosome Location	chr7:104643470-104643471
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SRPK2-1	chr7:104637584-104654636	NONHSAT122594

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1010340	0.81[CEU][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs1011468	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10228174	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10247691	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10252714	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10263499	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1029596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11981882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12534212	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12705296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1558048	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs17640472	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17640508	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap]
rs2074753	0.84[CEU][hapmap];0.86[YRI][hapmap]
rs2097942	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.89[EUR][1000 genomes]
rs2106500	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2299298	0.87[EUR][1000 genomes]
rs2299305	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs2299309	0.84[CEU][hapmap]
rs4602821	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4727618	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730066	0.90[CHD][hapmap];0.93[ASN][1000 genomes]
rs56016333	0.86[ASN][1000 genomes]
rs6466035	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67665940	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6947388	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949073	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs6950894	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[EUR][1000 genomes]
rs6972563	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap]
rs6974874	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs6976394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6980244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[EUR][1000 genomes]
rs7796945	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs888086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9918494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv1029283	chr7:104571741-104729168	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	132 gene(s)	inside rSNPs	diseases
2	nsv888927	chr7:104614664-104781644	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
3	esv2829879	chr7:104618318-104652671	Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv608068	chr7:104622402-104757483	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv437561	chr7:104626690-104647571	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1022083	chr7:104634376-104644391	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104625000-104647400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:104625200-104643800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:104627400-104643600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:104630800-104643600	Weak transcription	Fetal Kidney	kidney
5	chr7:104631600-104643600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:104633200-104643600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr7:104633600-104650400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr7:104634000-104647200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr7:104635600-104645600	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr7:104636400-104645400	Enhancers	Fetal Heart	heart
11	chr7:104636400-104649400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr7:104638200-104646800	Enhancers	Stomach Mucosa	stomach
13	chr7:104638400-104643800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr7:104638400-104645800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr7:104638600-104643800	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr7:104639400-104643600	Enhancers	Adipose Nuclei	Adipose
17	chr7:104639400-104649800	Genic enhancers	Fetal Intestine Small	intestine
18	chr7:104639800-104648800	Enhancers	Colon Smooth Muscle	Colon
19	chr7:104640000-104643800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:104640000-104646200	Enhancers	Liver	Liver
21	chr7:104640200-104645600	Enhancers	Brain Angular Gyrus	brain
22	chr7:104640200-104648600	Genic enhancers	Dnd41	blood
23	chr7:104640400-104643800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr7:104640600-104643600	Strong transcription	K562	blood
25	chr7:104640800-104643600	Enhancers	Brain Anterior Caudate	brain
26	chr7:104640800-104645800	Enhancers	Brain Hippocampus Middle	brain
27	chr7:104641000-104643600	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr7:104641400-104643600	Enhancers	Duodenum Mucosa	Duodenum
29	chr7:104641600-104643600	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr7:104641800-104643600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr7:104641800-104643600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr7:104641800-104643600	Weak transcription	Fetal Muscle Leg	muscle
33	chr7:104641800-104643600	Weak transcription	Gastric	stomach
34	chr7:104641800-104643600	Weak transcription	Spleen	Spleen
35	chr7:104641800-104643800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr7:104641800-104643800	Weak transcription	Right Ventricle	heart
37	chr7:104641800-104643800	Weak transcription	Thymus	Thymus
38	chr7:104641800-104646000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr7:104641800-104646000	Weak transcription	Lung	lung
40	chr7:104641800-104649000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr7:104641800-104651800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr7:104642000-104643600	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr7:104642000-104643600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr7:104642000-104643600	Enhancers	Rectal Smooth Muscle	rectum
45	chr7:104642000-104644200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr7:104642000-104644400	Weak transcription	Brain Germinal Matrix	brain
47	chr7:104642000-104650200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr7:104642000-104650600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr7:104642200-104644600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr7:104642200-104645200	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links