Variant report

Variant	rs12904815
Chromosome Location	chr15:45492118-45492119
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RPC155	chr15:45492117-45493821	Hela-S3	cervix:	n/a	n/a
2	REST	chr15:45492104-45493445	H1-neurons	neurons:	n/a	chr15:45493206-45493219 chr15:45493203-45493210
3	ATF2	chr15:45492093-45493483	GM12878	blood:	n/a	n/a
4	GTF3C2	chr15:45489873-45494042	Hela-S3	cervix:	n/a	n/a
5	REST	chr15:45489971-45493834	H1-neurons	neurons:	n/a	chr15:45493206-45493219 chr15:45491453-45491466 chr15:45493203-45493210
6	MYBL2	chr15:45492075-45493989	HepG2	liver:	n/a	n/a
7	ZNF384	chr15:45489912-45492916	K562	blood:	n/a	n/a
8	MAX	chr15:45492102-45493756	A549	lung:	n/a	n/a
9	SREBP2	chr15:45489970-45494276	GM12878	blood:	n/a	n/a
10	ZNF384	chr15:45492051-45492900	GM12878	blood:	n/a	n/a
11	FOXM1	chr15:45491975-45493782	GM12878	blood:	n/a	n/a
12	POLR2A	chr15:45490375-45493640	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr15:45490278-45493529	H1-neurons	neurons:	n/a	n/a
14	SIN3A	chr15:45490566-45493571	H1-hESC	embryonic stem cell:	n/a	n/a
15	MTA3	chr15:45492089-45494204	GM12878	blood:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:45478077..45482452-chr15:45491020..45494377,5	MCF-7	breast:
2	chr15:45490877..45493855-chr15:45879081..45881062,2	K562	blood:
3	chr15:45457346..45461990-chr15:45488766..45494297,11	MCF-7	breast:
4	chr15:45477456..45480320-chr15:45491100..45493481,2	MCF-7	breast:
5	chr15:45458639..45463256-chr15:45489443..45493548,9	K562	blood:
6	chr15:45491292..45493253-chr15:45693461..45696308,4	K562	blood:
7	chr15:45491035..45492770-chr15:45505625..45508217,2	K562	blood:
8	chr15:45490733..45493253-chr15:45692978..45696308,3	K562	blood:
9	chr15:45457899..45460285-chr15:45489261..45492223,4	MCF-7	breast:
10	chr15:45472426..45475821-chr15:45489773..45493159,3	K562	blood:
11	chr15:45472426..45474381-chr15:45491659..45493233,2	K562	blood:
12	chr15:45457999..45463256-chr15:45488727..45493013,8	K562	blood:
13	chr15:45491756..45494677-chr15:45570318..45572091,2	MCF-7	breast:
14	chr15:45472971..45475470-chr15:45491028..45492942,2	MCF-7	breast:
15	chr15:45489573..45492565-chr15:45693942..45696435,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DUOX1-1	chr15:45492056-45492156	ENSG00000259519.1

No data

Variant related genes	Relation type
ENSG00000259932	TF binding region
ENSG00000259520	Chromatin interaction
ENSG00000171763	Chromatin interaction
ENSG00000171766	Chromatin interaction
ENSG00000259539	Chromatin interaction
ENSG00000138606	Chromatin interaction
ENSG00000259338	Chromatin interaction
ENSG00000261709	Chromatin interaction
ENSG00000104164	Chromatin interaction
ENSG00000259519	Chromatin interaction
ENSG00000260170	Chromatin interaction

Extended variants
information (count: 140 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs10450969	0.82[EUR][1000 genomes]
rs10450970	0.84[EUR][1000 genomes]
rs10467979	0.85[EUR][1000 genomes]
rs10775129	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10851421	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10851422	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10851423	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11070444	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11070451	0.84[EUR][1000 genomes]
rs11634794	0.85[EUR][1000 genomes]
rs11636018	0.84[EUR][1000 genomes]
rs11636410	0.84[EUR][1000 genomes]
rs11636440	0.84[EUR][1000 genomes]
rs11639403	0.84[EUR][1000 genomes]
rs11854234	0.82[EUR][1000 genomes]
rs11854294	0.84[EUR][1000 genomes]
rs11854345	0.84[EUR][1000 genomes]
rs11854347	0.85[EUR][1000 genomes]
rs11854377	0.84[EUR][1000 genomes]
rs11854689	0.85[EUR][1000 genomes]
rs11854690	0.85[EUR][1000 genomes]
rs11855435	0.81[EUR][1000 genomes]
rs11855466	0.84[EUR][1000 genomes]
rs11857919	0.84[EUR][1000 genomes]
rs12323957	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12437603	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12440238	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12440321	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12440793	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12592055	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12593605	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12901114	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12902212	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12903149	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12904079	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12904265	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12904331	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12904591	0.81[EUR][1000 genomes]
rs12905053	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12905246	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12906537	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12906734	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12909987	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12910214	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12910270	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12910357	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12910591	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12911551	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12913123	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12915027	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12915804	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12915965	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12917187	0.84[EUR][1000 genomes]
rs13329225	0.84[EUR][1000 genomes]
rs13329228	0.85[EUR][1000 genomes]
rs1631533	0.85[EUR][1000 genomes]
rs1648285	0.85[EUR][1000 genomes]
rs1648286	0.85[EUR][1000 genomes]
rs1648287	0.86[EUR][1000 genomes]
rs1648289	0.86[EUR][1000 genomes]
rs1648295	0.85[EUR][1000 genomes]
rs1648302	0.89[EUR][1000 genomes]
rs16941017	0.83[EUR][1000 genomes]
rs1706763	0.83[EUR][1000 genomes]
rs1706764	0.85[EUR][1000 genomes]
rs1706832	0.85[EUR][1000 genomes]
rs1706834	0.86[EUR][1000 genomes]
rs1706835	0.85[EUR][1000 genomes]
rs1706837	0.85[EUR][1000 genomes]
rs2413775	0.83[EUR][1000 genomes]
rs2413776	0.83[EUR][1000 genomes]
rs2413778	0.84[EUR][1000 genomes]
rs2413780	0.84[EUR][1000 genomes]
rs2413782	0.84[EUR][1000 genomes]
rs2413786	0.85[EUR][1000 genomes]
rs2433227	0.85[EUR][1000 genomes]
rs2433228	0.85[EUR][1000 genomes]
rs2433229	0.85[EUR][1000 genomes]
rs2458224	0.85[EUR][1000 genomes]
rs2554453	0.82[EUR][1000 genomes]
rs2554454	0.85[EUR][1000 genomes]
rs2554455	0.85[EUR][1000 genomes]
rs2554456	0.85[EUR][1000 genomes]
rs2554457	0.85[EUR][1000 genomes]
rs2668737	0.85[EUR][1000 genomes]
rs2668751	0.85[EUR][1000 genomes]
rs28524974	0.84[EUR][1000 genomes]
rs28526629	0.85[EUR][1000 genomes]
rs28628668	0.82[EUR][1000 genomes]
rs28733848	0.85[EUR][1000 genomes]
rs28756676	0.84[EUR][1000 genomes]
rs28789819	0.84[EUR][1000 genomes]
rs28815867	0.84[EUR][1000 genomes]
rs28851791	0.84[EUR][1000 genomes]
rs28859291	0.84[EUR][1000 genomes]
rs28877685	0.84[EUR][1000 genomes]
rs28889270	0.84[EUR][1000 genomes]
rs28897155	0.84[EUR][1000 genomes]
rs28897234	0.81[EUR][1000 genomes]
rs2899378	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2899379	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3759892	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3759893	0.83[EUR][1000 genomes]
rs3759895	0.83[EUR][1000 genomes]
rs3959644	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs3985919	0.85[EUR][1000 genomes]
rs4238376	0.84[EUR][1000 genomes]
rs4238377	0.82[EUR][1000 genomes]
rs4270107	0.82[EUR][1000 genomes]
rs4439707	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4442750	0.82[EUR][1000 genomes]
rs4444275	0.82[EUR][1000 genomes]
rs4514617	0.84[EUR][1000 genomes]
rs4544188	0.84[EUR][1000 genomes]
rs4774542	0.85[EUR][1000 genomes]
rs4774550	0.84[EUR][1000 genomes]
rs4775819	0.85[EUR][1000 genomes]
rs4775822	0.84[EUR][1000 genomes]
rs4775823	0.84[EUR][1000 genomes]
rs4775826	0.84[EUR][1000 genomes]
rs4775831	0.84[EUR][1000 genomes]
rs4775832	0.84[EUR][1000 genomes]
rs4775834	0.84[EUR][1000 genomes]
rs4775835	0.84[EUR][1000 genomes]
rs4775836	0.84[EUR][1000 genomes]
rs4775837	0.84[EUR][1000 genomes]
rs4775844	0.84[EUR][1000 genomes]
rs55771002	0.84[EUR][1000 genomes]
rs55920042	0.84[EUR][1000 genomes]
rs62026665	0.83[AMR][1000 genomes]
rs7167326	0.81[EUR][1000 genomes]
rs7167731	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7169015	0.84[EUR][1000 genomes]
rs7171401	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7174913	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv904187	chr15:45438537-45507738	Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45489600-45494000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:45489800-45493400	Active TSS	A549	lung
3	chr15:45489800-45493600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr15:45489800-45493600	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr15:45489800-45493800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr15:45489800-45493800	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr15:45489800-45493800	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr15:45489800-45494000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr15:45490000-45493600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:45490000-45493600	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr15:45490000-45493600	Active TSS	Fetal Lung	lung
12	chr15:45490000-45493800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:45490000-45493800	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr15:45490000-45493800	Active TSS	Brain Anterior Caudate	brain
15	chr15:45490000-45493800	Active TSS	Fetal Kidney	kidney
16	chr15:45490000-45493800	Active TSS	K562	blood
17	chr15:45490000-45494000	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr15:45490200-45492200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr15:45490200-45493400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr15:45490200-45493400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:45490200-45493400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:45490200-45493400	Active TSS	Aorta	Aorta
23	chr15:45490200-45493400	Active TSS	Ovary	ovary
24	chr15:45490200-45493400	Active TSS	Psoas Muscle	Psoas
25	chr15:45490200-45493600	Active TSS	H1 Cell Line	embryonic stem cell
26	chr15:45490200-45493600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr15:45490200-45493600	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr15:45490200-45493600	Active TSS	Right Atrium	heart
29	chr15:45490200-45493600	Active TSS	GM12878-XiMat	blood
30	chr15:45490200-45493600	Active TSS	HSMMtube	muscle
31	chr15:45490200-45493600	Active TSS	NHDF-Ad	bronchial
32	chr15:45490200-45493800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr15:45490200-45493800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr15:45490200-45493800	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr15:45490200-45493800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr15:45490200-45493800	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr15:45490200-45494000	Active TSS	Brain Angular Gyrus	brain
38	chr15:45490200-45494400	Active TSS	Fetal Brain Female	brain
39	chr15:45490400-45493200	Active TSS	Sigmoid Colon	Sigmoid Colon
40	chr15:45490400-45493600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr15:45490400-45493600	Active TSS	Brain Cingulate Gyrus	brain
42	chr15:45490400-45493600	Active TSS	Colon Smooth Muscle	Colon
43	chr15:45490400-45493600	Active TSS	Left Ventricle	heart
44	chr15:45490400-45493600	Active TSS	Right Ventricle	heart
45	chr15:45490400-45493800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr15:45490400-45493800	Active TSS	Brain Substantia Nigra	brain
47	chr15:45490400-45494000	Active TSS	Brain Hippocampus Middle	brain
48	chr15:45490600-45493400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr15:45490600-45493600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:45491000-45492600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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