Variant report

Variant	rs12534212
Chromosome Location	chr7:104641241-104641242
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:104640833..104643034-chr7:104805707..104808413,2	K562	blood:

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

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1011468	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10228174	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10247691	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10252714	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10263499	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1029596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11978288	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11981882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12705296	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1558048	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17640472	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2074753	0.84[CEU][hapmap]
rs2097942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs2106500	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2299298	0.87[EUR][1000 genomes]
rs2299305	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2299309	0.84[CEU][hapmap]
rs4602821	0.93[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];0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730066	0.93[ASN][1000 genomes]
rs56016333	0.86[ASN][1000 genomes]
rs6466035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67665940	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6947388	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949073	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6950894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs6974874	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6976394	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6980244	0.96[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];0.87[EUR][1000 genomes]
rs7796945	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs888086	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9918494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv437995	chr7:104632980-104641241	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	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:122 , 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	chr7:104625400-104643000	Weak transcription	Fetal Brain Female	brain
4	chr7:104626200-104641600	Weak transcription	Brain Germinal Matrix	brain
5	chr7:104627400-104643600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:104630800-104641600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr7:104630800-104643600	Weak transcription	Fetal Kidney	kidney
8	chr7:104631600-104643600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr7:104632800-104641400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr7:104633000-104642600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:104633200-104643600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr7:104633400-104641400	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr7:104633600-104650400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr7:104634000-104647200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr7:104634400-104642800	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr7:104634400-104642800	Weak transcription	HSMMtube	muscle
17	chr7:104634800-104641800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr7:104635200-104642800	Weak transcription	NH-A	brain
19	chr7:104635400-104641400	Enhancers	Primary T cells from cord blood	blood
20	chr7:104635400-104641400	Weak transcription	Aorta	Aorta
21	chr7:104635400-104641800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr7:104635400-104642200	Weak transcription	Brain Substantia Nigra	brain
23	chr7:104635400-104643200	Weak transcription	HUVEC	blood vessel
24	chr7:104635600-104645600	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr7:104635800-104643400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr7:104636400-104641400	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr7:104636400-104645400	Enhancers	Fetal Heart	heart
28	chr7:104636400-104649400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr7:104636600-104641800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr7:104636800-104641400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr7:104636800-104641400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr7:104636800-104641400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr7:104637000-104643400	Weak transcription	HepG2	liver
34	chr7:104637200-104641400	Weak transcription	Thymus	Thymus
35	chr7:104637200-104641600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr7:104637200-104641800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr7:104637200-104643400	Weak transcription	Fetal Lung	lung
38	chr7:104638200-104646800	Enhancers	Stomach Mucosa	stomach
39	chr7:104638400-104643800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr7:104638400-104645800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr7:104638600-104643800	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr7:104639200-104642200	Genic enhancers	A549	lung
43	chr7:104639400-104641400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr7:104639400-104642600	Enhancers	Psoas Muscle	Psoas
45	chr7:104639400-104643400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr7:104639400-104643600	Enhancers	Adipose Nuclei	Adipose
47	chr7:104639400-104649800	Genic enhancers	Fetal Intestine Small	intestine
48	chr7:104639600-104642600	Genic enhancers	Fetal Intestine Large	intestine
49	chr7:104639800-104641800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr7:104639800-104648800	Enhancers	Colon Smooth Muscle	Colon

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