Variant report

Variant	rs1956517
Chromosome Location	chr14:37738427-37738428
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	chr14:37723949..37726058-chr14:37737860..37739770,2	MCF-7	breast:
2	chr14:37730985..37733871-chr14:37737549..37739404,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-537P22.1.1-1	chr14:37737668-37742505	l_969_chr14:37729807-37741737_76bGuttman_hES

Extended variants
information (count: 115 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1005539	1.00[EUR][1000 genomes]
rs1005540	1.00[EUR][1000 genomes]
rs10129341	1.00[EUR][1000 genomes]
rs10132652	1.00[EUR][1000 genomes]
rs10132727	1.00[EUR][1000 genomes]
rs10134672	1.00[EUR][1000 genomes]
rs10135014	1.00[EUR][1000 genomes]
rs10136240	1.00[EUR][1000 genomes]
rs10137554	1.00[EUR][1000 genomes]
rs10141822	1.00[EUR][1000 genomes]
rs10144237	1.00[EUR][1000 genomes]
rs10144304	1.00[EUR][1000 genomes]
rs10145246	1.00[EUR][1000 genomes]
rs10146919	1.00[EUR][1000 genomes]
rs1014880	1.00[EUR][1000 genomes]
rs10150559	1.00[EUR][1000 genomes]
rs10782386	1.00[EUR][1000 genomes]
rs11845464	0.87[EUR][1000 genomes]
rs11846576	0.87[EUR][1000 genomes]
rs11848827	1.00[EUR][1000 genomes]
rs11849999	1.00[EUR][1000 genomes]
rs12434053	1.00[EUR][1000 genomes]
rs12437318	1.00[EUR][1000 genomes]
rs12586942	1.00[EUR][1000 genomes]
rs12717263	1.00[EUR][1000 genomes]
rs1474887	1.00[EUR][1000 genomes]
rs1474888	1.00[EUR][1000 genomes]
rs1546973	1.00[EUR][1000 genomes]
rs1950518	1.00[EUR][1000 genomes]
rs1950525	1.00[EUR][1000 genomes]
rs1950528	1.00[EUR][1000 genomes]
rs1950535	1.00[EUR][1000 genomes]
rs1955932	1.00[EUR][1000 genomes]
rs1955933	1.00[EUR][1000 genomes]
rs1955935	1.00[EUR][1000 genomes]
rs1955937	1.00[EUR][1000 genomes]
rs1955953	1.00[EUR][1000 genomes]
rs1955954	1.00[EUR][1000 genomes]
rs1955956	1.00[EUR][1000 genomes]
rs1956518	0.87[AFR][1000 genomes]
rs1998019	1.00[EUR][1000 genomes]
rs2144582	1.00[EUR][1000 genomes]
rs2180252	1.00[EUR][1000 genomes]
rs2180253	1.00[EUR][1000 genomes]
rs2207861	1.00[EUR][1000 genomes]
rs2207863	1.00[EUR][1000 genomes]
rs2224155	1.00[EUR][1000 genomes]
rs2224157	1.00[EUR][1000 genomes]
rs2415390	0.87[EUR][1000 genomes]
rs2415392	1.00[EUR][1000 genomes]
rs2415394	1.00[EUR][1000 genomes]
rs2415395	1.00[EUR][1000 genomes]
rs2899856	1.00[EUR][1000 genomes]
rs2899858	1.00[EUR][1000 genomes]
rs34172996	1.00[EUR][1000 genomes]
rs41307090	1.00[EUR][1000 genomes]
rs4522332	1.00[EUR][1000 genomes]
rs4898593	1.00[EUR][1000 genomes]
rs4900779	1.00[EUR][1000 genomes]
rs4900823	1.00[EUR][1000 genomes]
rs4900834	1.00[EUR][1000 genomes]
rs57167835	0.87[EUR][1000 genomes]
rs57900485	0.87[EUR][1000 genomes]
rs58520096	1.00[EUR][1000 genomes]
rs59258105	1.00[EUR][1000 genomes]
rs59542560	0.87[EUR][1000 genomes]
rs59544181	0.87[EUR][1000 genomes]
rs60287404	1.00[EUR][1000 genomes]
rs6571804	1.00[EUR][1000 genomes]
rs6571805	1.00[EUR][1000 genomes]
rs6571809	1.00[EUR][1000 genomes]
rs7142072	1.00[EUR][1000 genomes]
rs7142933	1.00[EUR][1000 genomes]
rs7143412	1.00[EUR][1000 genomes]
rs7146631	1.00[EUR][1000 genomes]
rs7150214	1.00[EUR][1000 genomes]
rs7150986	0.87[EUR][1000 genomes]
rs7154479	1.00[EUR][1000 genomes]
rs7154977	1.00[EUR][1000 genomes]
rs7157931	1.00[EUR][1000 genomes]
rs7158473	1.00[EUR][1000 genomes]
rs7159514	1.00[ASW][hapmap];0.84[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap]
rs7160824	1.00[EUR][1000 genomes]
rs7161464	1.00[EUR][1000 genomes]
rs719135	1.00[EUR][1000 genomes]
rs8013329	1.00[EUR][1000 genomes]
rs8014311	1.00[EUR][1000 genomes]
rs8015886	1.00[EUR][1000 genomes]
rs8016309	1.00[EUR][1000 genomes]
rs8019167	1.00[EUR][1000 genomes]
rs8019673	1.00[EUR][1000 genomes]
rs8020631	1.00[EUR][1000 genomes]
rs8022961	1.00[EUR][1000 genomes]
rs987859	1.00[EUR][1000 genomes]
rs9989228	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530038	chr14:37590543-38336191	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv915783	chr14:37607836-38002966	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1036854	chr14:37609535-38013533	Active TSS ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv542045	chr14:37609535-38013533	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv901635	chr14:37623177-37782273	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	esv3528451	chr14:37631483-37771365	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv3527359	chr14:37631504-37771435	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	esv3370191	chr14:37631508-37771354	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	esv3527360	chr14:37631521-37771311	Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	esv3528462	chr14:37631535-37771345	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	esv3528473	chr14:37631543-37771255	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	esv3527361	chr14:37631554-37771408	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	esv3528484	chr14:37631599-37771228	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	esv3527363	chr14:37631608-37771230	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv901637	chr14:37702799-37743583	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv901638	chr14:37702799-37814824	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
17	esv1797813	chr14:37738197-37846877	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	esv1820642	chr14:37738197-37846877	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	esv1822817	chr14:37738197-37846877	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	esv1851834	chr14:37738197-37846877	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1956517	S100A10	trans	brain	seeQTL
rs1956517	SFRP2	trans	brain	seeQTL
rs1956517	PGAM2	trans	brain	seeQTL
rs1956517	KLK1	trans	brain	seeQTL
rs1956517	NUPR1	trans	brain	seeQTL
rs1956517	TPM1	trans	brain	seeQTL
rs1956517	SLC26A2	trans	brain	seeQTL
rs1956517	FGL2	trans	brain	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:37694800-37756400	Weak transcription	Aorta	Aorta
2	chr14:37716000-37770600	Weak transcription	A549	lung
3	chr14:37717800-37738600	Weak transcription	Fetal Intestine Small	intestine
4	chr14:37726800-37740000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr14:37727000-37740400	Weak transcription	HSMMtube	muscle
6	chr14:37732000-37739600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr14:37732200-37739800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr14:37733600-37758200	Weak transcription	Fetal Lung	lung
9	chr14:37735000-37742600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr14:37735600-37738600	Weak transcription	Brain Hippocampus Middle	brain
11	chr14:37736400-37744200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr14:37736800-37758400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr14:37737200-37744400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr14:37738000-37755000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr14:37738000-37756400	Weak transcription	Ovary	ovary
16	chr14:37738200-37739800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr14:37738200-37739800	Weak transcription	HUVEC	blood vessel
18	chr14:37738400-37757600	Weak transcription	Adipose Nuclei	Adipose

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