Variant report

Variant	rs12323957
Chromosome Location	chr15:45490773-45490774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:45490447..45491260-chr17:41444880..41445454,2	Hela-S3	cervix:
2	chr15:45481532..45483736-chr15:45488202..45490839,2	K562	blood:
3	chr15:45457346..45461990-chr15:45488766..45494297,11	MCF-7	breast:
4	chr15:45458639..45463256-chr15:45489443..45493548,9	K562	blood:
5	chr1:226250333..226250903-chr15:45490663..45491581,2	Hela-S3	cervix:
6	chr15:45489521..45491302-chr15:45567648..45569193,2	MCF-7	breast:
7	chr15:45490733..45493253-chr15:45692978..45696308,3	K562	blood:
8	chr15:45457899..45460285-chr15:45489261..45492223,4	MCF-7	breast:
9	chr15:45472426..45475821-chr15:45489773..45493159,3	K562	blood:
10	chr15:45489158..45491324-chr15:45514071..45516738,2	K562	blood:
11	chr15:45457999..45463256-chr15:45488727..45493013,8	K562	blood:
12	chr15:45484569..45487478-chr15:45489184..45491239,2	K562	blood:
13	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-DUOXA1-1	chr15:45490715-45491337	ENSG00000259932.1

No data

Variant related genes	Relation type
ENSG00000259519	Chromatin interaction
ENSG00000138606	Chromatin interaction
ENSG00000259539	Chromatin interaction
ENSG00000171763	Chromatin interaction
ENSG00000171766	Chromatin interaction
ENSG00000163041	Chromatin interaction

Extended variants
information (count: 153 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs10450969	0.89[EUR][1000 genomes]
rs10450970	0.91[EUR][1000 genomes]
rs10467979	0.93[EUR][1000 genomes]
rs10775129	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10851421	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10851422	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10851423	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11070444	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11070451	0.92[EUR][1000 genomes]
rs11634794	0.92[EUR][1000 genomes]
rs11636018	0.92[EUR][1000 genomes]
rs11636410	0.91[EUR][1000 genomes]
rs11636440	0.91[EUR][1000 genomes]
rs11639403	0.92[EUR][1000 genomes]
rs11854234	0.89[EUR][1000 genomes]
rs11854294	0.92[EUR][1000 genomes]
rs11854345	0.90[EUR][1000 genomes]
rs11854347	0.92[EUR][1000 genomes]
rs11854377	0.92[EUR][1000 genomes]
rs11854689	0.93[EUR][1000 genomes]
rs11854690	0.93[EUR][1000 genomes]
rs11855435	0.88[EUR][1000 genomes]
rs11855466	0.92[EUR][1000 genomes]
rs11857919	0.92[EUR][1000 genomes]
rs11858988	0.86[EUR][1000 genomes]
rs12437603	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440238	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12440321	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12440793	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12592055	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12593605	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12899786	0.80[YRI][hapmap]
rs12901114	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12902212	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903149	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12904079	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12904265	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904331	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12904591	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12904815	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12905053	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12905246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906537	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12906734	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12909987	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910214	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12910270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910357	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12910591	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12911551	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12913123	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12915027	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12915804	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12915965	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917187	0.92[EUR][1000 genomes]
rs13329225	0.92[EUR][1000 genomes]
rs13329228	0.92[EUR][1000 genomes]
rs1631533	0.93[EUR][1000 genomes]
rs1648285	0.93[EUR][1000 genomes]
rs1648286	0.93[EUR][1000 genomes]
rs1648287	0.93[EUR][1000 genomes]
rs1648289	0.93[EUR][1000 genomes]
rs1648295	0.92[EUR][1000 genomes]
rs1648302	0.98[EUR][1000 genomes]
rs16941017	0.91[EUR][1000 genomes]
rs1706763	0.90[EUR][1000 genomes]
rs1706764	0.93[EUR][1000 genomes]
rs1706821	0.80[EUR][1000 genomes]
rs1706822	0.80[EUR][1000 genomes]
rs1706832	0.93[EUR][1000 genomes]
rs1706834	0.93[EUR][1000 genomes]
rs1706835	0.93[EUR][1000 genomes]
rs1706837	0.93[EUR][1000 genomes]
rs2413775	0.90[EUR][1000 genomes]
rs2413776	0.91[EUR][1000 genomes]
rs2413778	0.92[EUR][1000 genomes]
rs2413780	0.92[EUR][1000 genomes]
rs2413782	0.92[EUR][1000 genomes]
rs2413786	0.93[EUR][1000 genomes]
rs2433227	0.93[EUR][1000 genomes]
rs2433228	0.93[EUR][1000 genomes]
rs2433229	0.93[EUR][1000 genomes]
rs2458224	0.93[EUR][1000 genomes]
rs2467838	0.83[EUR][1000 genomes]
rs2554453	0.90[EUR][1000 genomes]
rs2554454	0.93[EUR][1000 genomes]
rs2554455	0.93[EUR][1000 genomes]
rs2554456	0.93[EUR][1000 genomes]
rs2554457	0.93[EUR][1000 genomes]
rs2668737	0.93[EUR][1000 genomes]
rs2668751	0.93[EUR][1000 genomes]
rs28498330	0.82[EUR][1000 genomes]
rs28524974	0.91[EUR][1000 genomes]
rs28526629	0.92[EUR][1000 genomes]
rs28628668	0.90[EUR][1000 genomes]
rs28680861	0.83[EUR][1000 genomes]
rs28701495	0.81[EUR][1000 genomes]
rs28733848	0.93[EUR][1000 genomes]
rs28756676	0.92[EUR][1000 genomes]
rs28789819	0.92[EUR][1000 genomes]
rs28815867	0.92[EUR][1000 genomes]
rs28847337	0.85[EUR][1000 genomes]
rs28851791	0.92[EUR][1000 genomes]
rs28859291	0.92[EUR][1000 genomes]
rs28877685	0.92[EUR][1000 genomes]
rs28889270	0.92[EUR][1000 genomes]
rs28897155	0.92[EUR][1000 genomes]
rs28897234	0.88[EUR][1000 genomes]
rs2899378	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2899379	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3759892	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3759893	0.91[EUR][1000 genomes]
rs3759895	0.91[EUR][1000 genomes]
rs3959644	0.88[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3985919	0.93[EUR][1000 genomes]
rs4238376	0.92[EUR][1000 genomes]
rs4238377	0.89[EUR][1000 genomes]
rs4270107	0.89[EUR][1000 genomes]
rs4439707	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4442750	0.89[EUR][1000 genomes]
rs4444275	0.89[EUR][1000 genomes]
rs4514617	0.92[EUR][1000 genomes]
rs4544188	0.91[EUR][1000 genomes]
rs4774542	0.93[EUR][1000 genomes]
rs4774550	0.92[EUR][1000 genomes]
rs4775819	0.93[EUR][1000 genomes]
rs4775822	0.92[EUR][1000 genomes]
rs4775823	0.92[EUR][1000 genomes]
rs4775826	0.92[EUR][1000 genomes]
rs4775831	0.91[EUR][1000 genomes]
rs4775832	0.91[EUR][1000 genomes]
rs4775834	0.92[EUR][1000 genomes]
rs4775835	0.92[EUR][1000 genomes]
rs4775836	0.92[EUR][1000 genomes]
rs4775837	0.92[EUR][1000 genomes]
rs4775844	0.92[EUR][1000 genomes]
rs55771002	0.92[EUR][1000 genomes]
rs55920042	0.92[EUR][1000 genomes]
rs62026661	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62026665	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62026666	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7167326	0.88[EUR][1000 genomes]
rs7167731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169015	0.91[EUR][1000 genomes]
rs7171401	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7174913	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753414	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv427961	chr15:45338381-45491634	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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:123 , 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	chr15:45489800-45491000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr15:45489800-45491600	Active TSS	Fetal Intestine Small	intestine
4	chr15:45489800-45493400	Active TSS	A549	lung
5	chr15:45489800-45493600	Active TSS	H9 Cell Line	embryonic stem cell
6	chr15:45489800-45493600	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr15:45489800-45493800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr15:45489800-45493800	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr15:45489800-45493800	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr15:45489800-45494000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:45490000-45490800	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr15:45490000-45491000	Active TSS	HepG2	liver
13	chr15:45490000-45491200	Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr15:45490000-45491200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:45490000-45491200	Active TSS	Fetal Muscle Leg	muscle
16	chr15:45490000-45491200	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr15:45490000-45491400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:45490000-45491400	Active TSS	Primary T cells from cord blood	blood
19	chr15:45490000-45491400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:45490000-45491400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:45490000-45491400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:45490000-45491400	Active TSS	Adipose Nuclei	Adipose
23	chr15:45490000-45491400	Active TSS	Brain Germinal Matrix	brain
24	chr15:45490000-45491400	Active TSS	Stomach Smooth Muscle	stomach
25	chr15:45490000-45491600	Active TSS	Fetal Intestine Large	intestine
26	chr15:45490000-45491600	Active TSS	Fetal Stomach	stomach
27	chr15:45490000-45493600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:45490000-45493600	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr15:45490000-45493600	Active TSS	Fetal Lung	lung
30	chr15:45490000-45493800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:45490000-45493800	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr15:45490000-45493800	Active TSS	Brain Anterior Caudate	brain
33	chr15:45490000-45493800	Active TSS	Fetal Kidney	kidney
34	chr15:45490000-45493800	Active TSS	K562	blood
35	chr15:45490000-45494000	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr15:45490200-45490800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr15:45490200-45490800	Active TSS	Rectal Smooth Muscle	rectum
38	chr15:45490200-45491000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr15:45490200-45491200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr15:45490200-45491200	Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr15:45490200-45491200	Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr15:45490200-45491200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:45490200-45491200	Active TSS	Fetal Brain Male	brain
44	chr15:45490200-45491200	Active TSS	Fetal Muscle Trunk	muscle
45	chr15:45490200-45491200	Active TSS	Dnd41	blood
46	chr15:45490200-45491200	Active TSS	Monocytes-CD14+_RO01746	blood
47	chr15:45490200-45491200	Active TSS	NH-A	brain
48	chr15:45490200-45491400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:45490200-45491400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:45490200-45491400	Active TSS	Breast Myoepithelial Primary Cells	Breast

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