Variant report

Variant	rs4350625
Chromosome Location	chr17:19980665-19980666
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:19977490..19979005-chr17:19979596..19981343,2	K562	blood:
2	chr17:19980057..19981963-chr17:19993152..19995446,2	K562	blood:
3	chr17:19977490..19979191-chr17:19979596..19981343,3	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11204422	1.00[ASN][1000 genomes]
rs11654025	0.81[ASN][1000 genomes]
rs11869931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870381	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11870673	0.85[ASN][1000 genomes]
rs12449914	0.93[AMR][1000 genomes]
rs12451216	0.92[ASN][1000 genomes]
rs12451841	0.98[ASN][1000 genomes]
rs12453332	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12937327	0.95[AMR][1000 genomes]
rs12942179	1.00[ASN][1000 genomes]
rs12943904	0.90[AMR][1000 genomes]
rs12947713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12949710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468953	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17685923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17686798	0.88[ASN][1000 genomes]
rs17759041	0.93[AMR][1000 genomes]
rs17759609	0.91[AMR][1000 genomes]
rs17759959	0.90[ASN][1000 genomes]
rs34370440	0.98[ASN][1000 genomes]
rs34756775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35041742	0.85[ASN][1000 genomes]
rs35124809	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35156798	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35191778	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35244101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35317166	0.95[AMR][1000 genomes]
rs35493088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35770292	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35915823	0.95[AMR][1000 genomes]
rs36051592	0.87[ASN][1000 genomes]
rs3862151	0.93[AMR][1000 genomes]
rs4341795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4346259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4471741	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924802	0.95[AMR][1000 genomes]
rs4924808	0.92[ASN][1000 genomes]
rs4925071	0.93[AMR][1000 genomes]
rs4925074	0.93[AMR][1000 genomes]
rs4925075	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925082	0.98[ASN][1000 genomes]
rs4925084	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4925088	0.84[ASN][1000 genomes]
rs56371654	0.95[AMR][1000 genomes]
rs57146223	0.80[ASN][1000 genomes]
rs62067488	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215803	1.00[ASN][1000 genomes]
rs7503407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8066705	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs8068484	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8074791	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs8075343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8081817	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888424	1.00[ASN][1000 genomes]
rs972966	0.88[ASN][1000 genomes]
rs9901125	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers 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	nsv907871	chr17:19927699-20088492	Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv482438	chr17:19934376-20089005	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv907872	chr17:19945841-19996140	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1056224	chr17:19946604-19993026	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv543258	chr17:19946604-19993026	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1066594	chr17:19947874-19986671	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv543259	chr17:19947874-19986671	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv833395	chr17:19969959-20124084	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	esv2762522	chr17:19976462-19996429	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4350625	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19976200-19988000	Weak transcription	Gastric	stomach
2	chr17:19976200-19989400	Weak transcription	Lung	lung
3	chr17:19977600-19989600	Weak transcription	K562	blood
4	chr17:19977800-19983000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr17:19978000-19984000	Weak transcription	Brain Angular Gyrus	brain
6	chr17:19978000-19988200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr17:19978400-19981800	Weak transcription	Primary T cells from cord blood	blood
8	chr17:19978800-19980800	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr17:19978800-20000000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr17:19979000-19988200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr17:19979800-19980800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr17:19979800-19980800	Enhancers	A549	lung
13	chr17:19980000-19980800	Enhancers	Brain Cingulate Gyrus	brain
14	chr17:19980200-19980800	Enhancers	NHLF	lung
15	chr17:19980200-19988200	Weak transcription	Brain Hippocampus Middle	brain
16	chr17:19980400-19980800	Weak transcription	Aorta	Aorta
17	chr17:19980400-19981000	Active TSS	GM12878-XiMat	blood
18	chr17:19980400-19981200	Enhancers	Ovary	ovary
19	chr17:19980400-19981600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr17:19980400-19981600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr17:19980400-19982600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr17:19980400-19983400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr17:19980600-19981200	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr17:19980600-19981600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr17:19980600-19981600	Enhancers	Adipose Nuclei	Adipose
26	chr17:19980600-19982600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr17:19980600-19986400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr17:19980600-19994600	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links