Variant report

Variant	rs4346259
Chromosome Location	chr17:19977414-19977415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11204422	1.00[ASN][1000 genomes]
rs11869931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12937327	0.95[AMR][1000 genomes];0.81[EUR][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];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]
rs17685923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];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]
rs4341795	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]
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];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	0.98[ASN][1000 genomes]
rs4925084	0.95[AMR][1000 genomes];0.96[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];1.00[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];0.99[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];1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8081817	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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
rs4346259	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19974200-19978000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr17:19975200-19977600	Enhancers	K562	blood
3	chr17:19975400-19978000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr17:19975400-19978800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr17:19975600-19977600	Enhancers	Brain Germinal Matrix	brain
6	chr17:19975800-19977600	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr17:19975800-19978000	Enhancers	NHDF-Ad	bronchial
8	chr17:19975800-19978200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr17:19976000-19978200	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr17:19976000-19978200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr17:19976200-19977800	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr17:19976200-19978000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr17:19976200-19978200	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr17:19976200-19988000	Weak transcription	Gastric	stomach
15	chr17:19976200-19989400	Weak transcription	Lung	lung
16	chr17:19976400-19977600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr17:19976400-19977600	Enhancers	H1 Cell Line	embryonic stem cell
18	chr17:19976400-19977800	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr17:19976400-19978000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr17:19976400-19978000	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr17:19976400-19978200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr17:19976400-19978200	Flanking Active TSS	GM12878-XiMat	blood
23	chr17:19976600-19977600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr17:19976600-19977600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
25	chr17:19976600-19978000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr17:19976600-19978000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr17:19976600-19978200	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr17:19976600-19978200	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr17:19976600-19978200	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr17:19976600-19978200	Active TSS	Monocytes-CD14+_RO01746	blood
31	chr17:19976800-19977600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr17:19976800-19977600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr17:19976800-19977600	Enhancers	Esophagus	oesophagus
34	chr17:19976800-19977600	Flanking Active TSS	Osteobl	bone
35	chr17:19976800-19977800	Active TSS	Primary monocytes fromperipheralblood	blood
36	chr17:19976800-19978000	Active TSS	Brain Angular Gyrus	brain
37	chr17:19976800-19978000	Active TSS	Brain Anterior Caudate	brain
38	chr17:19976800-19978000	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr17:19976800-19978000	Enhancers	Fetal Lung	lung
40	chr17:19976800-19978000	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr17:19976800-19978800	Active TSS	Brain Hippocampus Middle	brain
42	chr17:19976800-19979000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr17:19977000-19977600	Active TSS	Fetal Stomach	stomach
44	chr17:19977000-19977600	Flanking Active TSS	Ovary	ovary
45	chr17:19977000-19977600	Active TSS	Psoas Muscle	Psoas
46	chr17:19977000-19977800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr17:19977000-19977800	Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr17:19977000-19977800	Enhancers	NHLF	lung
49	chr17:19977000-19978000	Active TSS	Duodenum Mucosa	Duodenum
50	chr17:19977000-19978000	Active TSS	Fetal Muscle Trunk	muscle

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