Variant report

Variant	rs1023924
Chromosome Location	chr15:73438622-73438623
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	chr15:73433416..73435936-chr15:73436842..73439135,2	K562	blood:

Variant related genes	Relation type
ENSG00000259691	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1038137	0.85[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10438294	0.81[CHB][hapmap];0.94[CHD][hapmap]
rs10467948	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10467949	0.86[CHD][hapmap]
rs11072403	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072406	0.87[ASN][1000 genomes]
rs1116880	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11634147	0.80[AMR][1000 genomes]
rs12050774	0.91[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12902768	0.88[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs12907139	0.80[JPT][hapmap]
rs13379875	0.85[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap]
rs1479338	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1479339	1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1479340	0.88[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes]
rs1564345	0.88[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap]
rs17762146	0.85[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs17762516	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17762600	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17829830	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17829836	0.81[AMR][1000 genomes]
rs17829957	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1812835	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1871385	0.88[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs1964543	0.85[EUR][1000 genomes]
rs2046017	0.86[CHD][hapmap]
rs2127277	0.88[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes]
rs2169951	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2251205	0.86[CHD][hapmap]
rs2415147	0.88[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs2415148	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2899784	0.88[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes]
rs34013312	0.80[ASN][1000 genomes]
rs35450875	0.84[ASN][1000 genomes]
rs3736510	0.88[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs3743489	0.87[CHB][hapmap]
rs3784793	1.00[CHB][hapmap]
rs3784801	0.86[CHB][hapmap];0.80[AMR][1000 genomes]
rs3985587	0.80[AMR][1000 genomes]
rs3985588	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4132535	0.83[CHD][hapmap]
rs4132536	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4375637	0.80[CHB][hapmap]
rs4545783	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4609810	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4776624	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4776625	0.81[AMR][1000 genomes]
rs4777589	0.86[CHD][hapmap]
rs4777590	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4777598	0.80[AMR][1000 genomes]
rs55646651	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55836604	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55853625	0.80[AMR][1000 genomes]
rs55868723	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs55925663	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55939596	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56215298	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56269104	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56348595	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56377702	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58060856	0.81[AMR][1000 genomes]
rs59066156	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62015500	0.83[AMR][1000 genomes]
rs62015502	0.81[AMR][1000 genomes]
rs62016797	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62016803	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62016805	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62016806	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62016808	0.85[EUR][1000 genomes]
rs62016809	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62016811	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62016813	0.85[EUR][1000 genomes]
rs62016814	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62016849	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62016851	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62016853	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62016854	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62017774	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62017776	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7165610	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7169083	0.88[CHB][hapmap];0.87[JPT][hapmap]
rs7172021	0.88[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes]
rs7172396	0.87[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs7175329	0.86[CHD][hapmap]
rs74022925	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs74025262	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs747872	0.88[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs747873	0.87[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs8024575	0.87[ASN][1000 genomes]
rs8026121	0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8026579	0.81[JPT][hapmap]
rs8035925	0.80[ASN][1000 genomes]
rs8042700	0.88[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs922516	0.86[CHD][hapmap]
rs9806496	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9920186	0.83[CHD][hapmap]
rs9972347	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3352103	chr15:73191535-73454001	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv904338	chr15:73313691-73483718	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv517966	chr15:73349633-73488753	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv525462	chr15:73349633-73563495	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv904339	chr15:73375847-73483718	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv904340	chr15:73375847-73524629	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv904341	chr15:73390790-73483718	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv904342	chr15:73390790-73524629	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv527236	chr15:73421239-73469535	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1023924	THAP10	cis	cerebellum	SCAN
rs1023924	GRAMD2	cis	parietal	SCAN
rs1023924	CIITA	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73396400-73444600	Weak transcription	Psoas Muscle	Psoas
2	chr15:73401400-73480200	Weak transcription	Right Ventricle	heart
3	chr15:73403000-73443400	Weak transcription	Fetal Kidney	kidney
4	chr15:73404200-73442600	Weak transcription	Left Ventricle	heart
5	chr15:73408000-73443400	Weak transcription	Adipose Nuclei	Adipose
6	chr15:73413600-73446400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr15:73414000-73440000	Weak transcription	Fetal Brain Female	brain
8	chr15:73414200-73445600	Weak transcription	Brain Substantia Nigra	brain
9	chr15:73414400-73458200	Weak transcription	Colonic Mucosa	Colon
10	chr15:73415400-73446600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:73416000-73453200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr15:73416600-73444600	Weak transcription	Fetal Muscle Leg	muscle
13	chr15:73416600-73444600	Weak transcription	Lung	lung
14	chr15:73416800-73448800	Weak transcription	Ovary	ovary
15	chr15:73417000-73443000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr15:73421000-73443200	Weak transcription	Brain Angular Gyrus	brain
17	chr15:73423400-73445400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:73423400-73448800	Weak transcription	Pancreas	Pancrea
19	chr15:73423600-73443200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr15:73423600-73444600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:73424200-73449200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:73425200-73447200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:73429000-73456600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr15:73429200-73449200	Weak transcription	Gastric	stomach
25	chr15:73429400-73447200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr15:73430200-73466600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr15:73431400-73443000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:73431800-73453800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr15:73432600-73448600	Weak transcription	Fetal Brain Male	brain
30	chr15:73433200-73440000	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr15:73435000-73444600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr15:73435600-73439200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr15:73435600-73443200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr15:73435600-73447200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:73435800-73448800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr15:73436000-73438800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:73436000-73439400	Weak transcription	Aorta	Aorta
38	chr15:73436000-73443200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr15:73436000-73444600	Weak transcription	Fetal Stomach	stomach
40	chr15:73436000-73446400	Weak transcription	Liver	Liver
41	chr15:73436200-73439800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr15:73436200-73443800	Weak transcription	Fetal Intestine Small	intestine
43	chr15:73436800-73443000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr15:73437000-73439000	Weak transcription	Brain Hippocampus Middle	brain
45	chr15:73437400-73439000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr15:73437600-73438800	Strong transcription	Fetal Lung	lung
47	chr15:73438000-73439400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:73438000-73439600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr15:73438200-73439600	Enhancers	Brain Anterior Caudate	brain
50	chr15:73438600-73441200	Weak transcription	Fetal Intestine Large	intestine

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