Variant report

Variant	rs8075343
Chromosome Location	chr17:19975487-19975488
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr17:19975425-19975672	HepG2	liver:	n/a	chr17:19975547-19975560
2	JUND	chr17:19975406-19975692	K562	blood:	n/a	n/a
3	JUND	chr17:19975379-19975693	HepG2	liver:	n/a	n/a
4	TAL1	chr17:19975373-19975571	K562	blood:	n/a	n/a
5	MYC	chr17:19975450-19975667	K562	blood:	n/a	n/a
6	MYC	chr17:19975462-19975626	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
SPECC1	TF binding region

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs11204422	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11867585	0.83[JPT][hapmap]
rs11869931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870381	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12453332	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12937327	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12942179	0.83[JPT][hapmap];1.00[ASN][1000 genomes]
rs12943904	0.90[AMR][1000 genomes]
rs12947713	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];1.00[ASN][1000 genomes]
rs12949710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468953	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1638526	0.90[JPT][hapmap]
rs17685923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17686798	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17759041	0.93[AMR][1000 genomes]
rs17759609	0.91[AMR][1000 genomes]
rs17759959	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2072337	0.90[JPT][hapmap]
rs28424266	0.90[JPT][hapmap]
rs34370440	0.98[ASN][1000 genomes]
rs34756775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35156798	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35191778	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35244101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35770292	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35915823	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36051592	0.87[ASN][1000 genomes]
rs3862151	0.93[AMR][1000 genomes]
rs4141185	0.90[JPT][hapmap]
rs4341795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4346259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4350625	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4570919	0.82[JPT][hapmap]
rs4924802	0.95[AMR][1000 genomes]
rs4924808	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4925071	0.93[AMR][1000 genomes]
rs4925074	0.93[AMR][1000 genomes]
rs4925075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925082	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4925084	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4925088	0.82[JPT][hapmap];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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587207	1.00[JPT][hapmap]
rs7207459	1.00[JPT][hapmap]
rs7209653	0.90[JPT][hapmap]
rs7215803	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7224875	1.00[JPT][hapmap]
rs7225249	0.91[JPT][hapmap]
rs7503407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8066705	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs8068484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8074791	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs8080190	1.00[JPT][hapmap]
rs8081817	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888424	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs972966	0.88[ASN][1000 genomes]
rs9897653	0.83[JPT][hapmap]
rs9901125	0.98[ASN][1000 genomes]
rs9901294	0.90[JPT][hapmap]
rs9915039	1.00[JPT][hapmap]
rs9944451	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8075343	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19968000-19977000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr17:19968200-19977000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr17:19969000-19975600	Weak transcription	Lung	lung
4	chr17:19969000-19975600	Weak transcription	Right Atrium	heart
5	chr17:19969200-19976600	Weak transcription	Aorta	Aorta
6	chr17:19969600-19975600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr17:19970000-19975600	Weak transcription	Fetal Muscle Leg	muscle
8	chr17:19970200-19975800	Weak transcription	NHDF-Ad	bronchial
9	chr17:19970400-19975600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr17:19970400-19975600	Weak transcription	Adipose Nuclei	Adipose
11	chr17:19973600-19976000	Weak transcription	Primary T cells from cord blood	blood
12	chr17:19974200-19978000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr17:19974800-19975600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr17:19974800-19976000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr17:19975000-19976400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr17:19975000-19976600	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr17:19975200-19975800	Genic enhancers	A549	lung
18	chr17:19975200-19976000	Enhancers	Primary hematopoietic stem cells	blood
19	chr17:19975200-19976000	Enhancers	Fetal Heart	heart
20	chr17:19975200-19976600	Enhancers	Brain Hippocampus Middle	brain
21	chr17:19975200-19976600	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr17:19975200-19976600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr17:19975200-19976800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr17:19975200-19977000	Enhancers	Brain Cingulate Gyrus	brain
25	chr17:19975200-19977000	Enhancers	Ovary	ovary
26	chr17:19975200-19977600	Enhancers	K562	blood
27	chr17:19975400-19975600	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr17:19975400-19976000	Enhancers	Left Ventricle	heart
29	chr17:19975400-19976400	Enhancers	GM12878-XiMat	blood
30	chr17:19975400-19976600	Enhancers	Brain Anterior Caudate	brain
31	chr17:19975400-19976800	Enhancers	Fetal Thymus	thymus
32	chr17:19975400-19977000	Enhancers	Brain Substantia Nigra	brain
33	chr17:19975400-19978000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr17:19975400-19978800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links