Variant report

Variant	rs11871651
Chromosome Location	chr17:19997425-19997426
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19995540..19998202-chr2:209032220..209035134,2	MCF-7	breast:

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10083856	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1034904	0.84[AMR][1000 genomes]
rs11867585	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11868084	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11868116	0.82[EUR][1000 genomes]
rs11869616	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11870111	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12936443	0.82[EUR][1000 genomes]
rs16960697	0.82[EUR][1000 genomes]
rs1859407	0.81[EUR][1000 genomes]
rs1860302	0.81[AMR][1000 genomes]
rs2013443	0.82[EUR][1000 genomes]
rs2042046	0.82[EUR][1000 genomes]
rs2108979	0.81[AMR][1000 genomes]
rs2108980	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2189709	0.81[EUR][1000 genomes]
rs2526463	0.81[EUR][1000 genomes]
rs2703795	0.80[EUR][1000 genomes]
rs28603224	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28637614	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28666381	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28807825	0.86[AMR][1000 genomes]
rs34290687	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34291370	0.82[AMR][1000 genomes]
rs34401389	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35003563	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35313716	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36077949	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3862152	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3888318	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3909258	0.86[AMR][1000 genomes]
rs4005937	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4267380	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4479309	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4570919	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4924801	0.84[AMR][1000 genomes]
rs4924803	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924806	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925065	0.84[AMR][1000 genomes]
rs4925066	0.84[AMR][1000 genomes]
rs4925067	0.84[AMR][1000 genomes]
rs4925069	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4925072	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4925073	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4925077	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4925079	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925081	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925085	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925086	0.82[EUR][1000 genomes]
rs4925087	0.82[EUR][1000 genomes]
rs4925090	0.80[EUR][1000 genomes]
rs4925091	0.80[EUR][1000 genomes]
rs55705283	0.82[EUR][1000 genomes]
rs62066865	0.82[EUR][1000 genomes]
rs62066870	0.80[EUR][1000 genomes]
rs62067555	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6587219	0.82[EUR][1000 genomes]
rs7207625	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7208025	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208365	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208635	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7209734	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7211535	0.81[AMR][1000 genomes]
rs7212500	0.82[EUR][1000 genomes]
rs7216599	0.82[EUR][1000 genomes]
rs7216794	0.82[EUR][1000 genomes]
rs7219908	0.82[EUR][1000 genomes]
rs7222984	0.83[EUR][1000 genomes]
rs7222987	0.80[EUR][1000 genomes]
rs7223305	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8065337	0.83[AMR][1000 genomes]
rs8066143	0.82[EUR][1000 genomes]
rs8067545	0.82[AMR][1000 genomes]
rs8078716	0.82[EUR][1000 genomes]
rs8080649	0.80[EUR][1000 genomes]
rs888423	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs918227	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs918228	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9889743	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9891739	0.86[AMR][1000 genomes]
rs9893832	0.82[EUR][1000 genomes]
rs9896411	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9897246	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9897653	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9898080	0.82[EUR][1000 genomes]
rs9901336	0.80[EUR][1000 genomes]
rs9901796	0.80[EUR][1000 genomes]
rs9902032	0.83[EUR][1000 genomes]
rs9907788	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9912775	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9915758	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9944451	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
rs11871651	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19978800-20000000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:19990200-19998800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:19993400-20006400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:19993600-19998600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr17:19993600-20000000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr17:19993600-20003600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr17:19993800-19998600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr17:19993800-19998800	Weak transcription	Spleen	Spleen
9	chr17:19993800-20000600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr17:19993800-20001600	Weak transcription	Lung	lung
11	chr17:19993800-20006400	Weak transcription	Esophagus	oesophagus
12	chr17:19993800-20008800	Weak transcription	GM12878-XiMat	blood
13	chr17:19994000-19997800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr17:19994600-19998400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr17:19994600-19998600	Enhancers	Brain Hippocampus Middle	brain
16	chr17:19995000-20000000	Weak transcription	Right Ventricle	heart
17	chr17:19995000-20001200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr17:19995200-19998200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr17:19995200-19998800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr17:19995400-19998400	Enhancers	Brain Angular Gyrus	brain
21	chr17:19995400-19998600	Enhancers	Adipose Nuclei	Adipose
22	chr17:19995600-19997600	Enhancers	Ovary	ovary
23	chr17:19995600-19998400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr17:19995800-19998200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr17:19995800-19998800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr17:19996000-19997800	Weak transcription	NHLF	lung
27	chr17:19996000-19998200	Weak transcription	NHDF-Ad	bronchial
28	chr17:19996000-19998200	Weak transcription	Osteobl	bone
29	chr17:19996200-19998200	Weak transcription	Brain Substantia Nigra	brain
30	chr17:19996200-19998200	Weak transcription	NH-A	brain
31	chr17:19996600-19997600	Weak transcription	Fetal Muscle Leg	muscle
32	chr17:19996600-19997800	Weak transcription	A549	lung
33	chr17:19996600-20000800	Weak transcription	Aorta	Aorta
34	chr17:19996800-19997600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr17:19996800-19997600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
36	chr17:19996800-19997600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr17:19996800-19998200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr17:19996800-19998200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr17:19996800-19998200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr17:19996800-19998400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr17:19996800-19998400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr17:19996800-19998800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr17:19996800-19998800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr17:19996800-19998800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr17:19996800-19999600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr17:19997000-19998200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr17:19997000-19998200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr17:19997000-19998400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr17:19997000-19998400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr17:19997000-19998400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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