Variant report

Variant	rs1645
Chromosome Location	chr15:50641824-50641825
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr15:50641598-50641846	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr15:50641221-50643664	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr15:50641547-50641904	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr15:50641549-50641891	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr15:50641590-50641881	MCF10A-Er-Src	breast:	n/a	n/a
6	ARID3A	chr15:50641786-50641922	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:50474061..50475974-chr15:50641012..50643370,2	MCF-7	breast:
2	chr15:50641443..50644268-chr15:50716209..50717916,2	MCF-7	breast:
3	chr15:50487139..50490001-chr15:50641333..50643043,2	K562	blood:
4	chr15:50625762..50628715-chr15:50641413..50643751,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HDC-2	chr15:50641135-50647076	NONHSAT042404

No data

Variant related genes	Relation type
ENSG00000271819	TF binding region
ENSG00000138592	Chromatin interaction
ENSG00000104043	Chromatin interaction
ENSG00000140284	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10152534	0.84[EUR][1000 genomes]
rs10220734	0.88[EUR][1000 genomes]
rs11070766	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11629603	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630045	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11630063	0.86[ASN][1000 genomes]
rs11631197	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11631985	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632019	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11632703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11633903	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs11636564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11636908	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11637901	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11637975	0.91[ASN][1000 genomes]
rs11638319	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs11638432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11638564	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11852487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11853236	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11855823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12594956	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs12902318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906304	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12908591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12909337	0.95[ASN][1000 genomes]
rs12910368	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12910586	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12912679	0.95[ASN][1000 genomes]
rs12912969	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12913144	0.83[EUR][1000 genomes]
rs12923	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16963604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16963612	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17508371	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17509944	1.00[JPT][hapmap]
rs1797311	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs1972699	0.84[EUR][1000 genomes]
rs1972700	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2033115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28372114	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28408662	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28451583	0.91[ASN][1000 genomes]
rs28453939	0.87[ASN][1000 genomes]
rs28531946	0.87[ASN][1000 genomes]
rs28534445	0.95[ASN][1000 genomes]
rs28609286	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28669213	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28688566	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28690939	0.95[ASN][1000 genomes]
rs28715646	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716586	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28719982	0.95[ASN][1000 genomes]
rs28886692	0.90[EUR][1000 genomes]
rs34143694	0.95[ASN][1000 genomes]
rs34197276	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34312018	0.91[ASN][1000 genomes]
rs34405772	0.91[ASN][1000 genomes]
rs34590486	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35000991	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35013067	0.82[ASN][1000 genomes]
rs35024305	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35033384	0.91[ASN][1000 genomes]
rs35168369	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35354250	0.95[ASN][1000 genomes]
rs35446819	0.87[ASN][1000 genomes]
rs35453213	0.95[ASN][1000 genomes]
rs35777196	0.90[EUR][1000 genomes]
rs3784297	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs4774559	0.95[ASN][1000 genomes]
rs4775872	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4775873	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4775874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4775875	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4775876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4775877	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526952	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs535648	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs62022571	0.80[ASN][1000 genomes]
rs62022573	0.85[EUR][1000 genomes]
rs6493425	0.89[EUR][1000 genomes]
rs6493427	0.82[EUR][1000 genomes]
rs6493429	1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6493430	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs7163457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164375	0.86[ASN][1000 genomes]
rs7164377	0.86[ASN][1000 genomes]
rs7164798	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7168233	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs7173127	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7175150	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7176792	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7179756	0.81[AMR][1000 genomes]
rs7183422	0.91[ASN][1000 genomes]
rs73399285	0.91[ASN][1000 genomes]
rs8024514	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8025367	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026571	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026785	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs8027367	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030036	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs8030952	0.91[ASN][1000 genomes]
rs8031431	0.87[EUR][1000 genomes]
rs8034597	0.91[ASN][1000 genomes]
rs8034615	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036354	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8039829	0.89[EUR][1000 genomes]
rs8042053	0.91[ASN][1000 genomes]
rs8042451	0.84[EUR][1000 genomes]
rs8042845	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs8043257	0.84[EUR][1000 genomes]
rs8043475	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs1645	CTD-3110H11.1	cis	Skin Sun Exposed Lower leg	GTEx
rs1645	CTD-3110H11.1	cis	Artery Tibial	GTEx
rs1645	CTD-3110H11.1	cis	Muscle Skeletal	GTEx
rs1645	GABPB2	cis	uninvolved skin	skin_eQTL
rs1645	GABPB1-AS1	cis	Stomach	GTEx
rs1645	CTD-3110H11.1	cis	Esophagus Muscularis	GTEx
rs1645	GABPB2	cis	lesional skin	skin_eQTL
rs1645	CTD-3110H11.1	cis	Thyroid	GTEx
rs1645	CTD-3110H11.1	cis	lung	GTEx
rs1645	GABPB1-AS1	cis	Artery Tibial	GTEx
rs1645	GABPB1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs1645	GABPB1-AS1	cis	Adipose Subcutaneous	GTEx
rs1645	CTD-3110H11.1	cis	Adipose Subcutaneous	GTEx
rs1645	GABPB1-AS1	cis	Nerve Tibial	GTEx
rs1645	CTD-3110H11.1	cis	Nerve Tibial	GTEx
rs1645	GABPB2	cis	normal skin	skin_eQTL
rs1645	GABPB1-AS1	cis	lung	GTEx
rs1645	GABPB1-AS1	cis	Esophagus Mucosa	GTEx
rs1645	CTD-3110H11.1	cis	Esophagus Mucosa	GTEx
rs1645	GABPB1-AS1	cis	Muscle Skeletal	GTEx
rs1645	GABPB1-AS1	cis	Esophagus Muscularis	GTEx
rs1645	GABPB1-AS1	cis	Whole Blood	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50600800-50643000	Weak transcription	Fetal Thymus	thymus
2	chr15:50600800-50643400	Weak transcription	Fetal Muscle Leg	muscle
3	chr15:50600800-50644200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:50600800-50644600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:50601400-50642800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:50608800-50642800	Weak transcription	Hela-S3	cervix
7	chr15:50615200-50644000	Weak transcription	HSMMtube	muscle
8	chr15:50618200-50642400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr15:50618400-50646000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:50621200-50646000	Weak transcription	Gastric	stomach
11	chr15:50622000-50642400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr15:50623400-50643000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:50623800-50644200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:50623800-50645600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr15:50624000-50644000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:50624000-50644000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:50624000-50644000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr15:50627600-50642400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:50627600-50643000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr15:50627800-50643600	Weak transcription	Lung	lung
21	chr15:50628400-50643600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr15:50629000-50642800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr15:50630000-50643600	Weak transcription	Placenta	Placenta
24	chr15:50631000-50643400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:50631400-50643400	Weak transcription	Fetal Stomach	stomach
26	chr15:50631400-50643800	Weak transcription	Fetal Intestine Small	intestine
27	chr15:50631600-50642400	Weak transcription	Thymus	Thymus
28	chr15:50633800-50645600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:50634400-50642200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr15:50634400-50642200	Weak transcription	Small Intestine	intestine
31	chr15:50635800-50643600	Weak transcription	Psoas Muscle	Psoas
32	chr15:50636400-50642400	Weak transcription	Fetal Lung	lung
33	chr15:50636800-50642200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr15:50638600-50642800	Weak transcription	Stomach Mucosa	stomach
35	chr15:50638800-50644000	Weak transcription	HMEC	breast
36	chr15:50638800-50644600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:50639000-50642600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:50639200-50642200	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr15:50639200-50644000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:50639400-50642200	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr15:50639400-50643400	Weak transcription	Left Ventricle	heart
42	chr15:50639600-50642200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr15:50639800-50642400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr15:50639800-50643000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr15:50640000-50642800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:50640600-50644000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr15:50640800-50642000	Enhancers	Primary B cells from cord blood	blood
48	chr15:50640800-50642000	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr15:50640800-50642200	Enhancers	Fetal Brain Male	brain
50	chr15:50640800-50642400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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