Variant report

Variant	rs1866400
Chromosome Location	chr15:41524236-41524237
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr15:41522761-41524259	K562	blood:	n/a	n/a
2	JUN	chr15:41522498-41524441	K562	blood:	n/a	chr15:41522968-41522977 chr15:41523399-41523408 chr15:41522875-41522889
3	RFX5	chr15:41522509-41524320	SK-N-SH	brain:	n/a	chr15:41523947-41523963 chr15:41522967-41522976
4	CUX1	chr15:41524001-41524269	K562	blood:	n/a	n/a
5	MAZ	chr15:41522655-41524296	IMR90	lung:	n/a	chr15:41523087-41523096
6	MXI1	chr15:41522442-41524490	SK-N-SH	brain:	n/a	n/a
7	HCFC1	chr15:41522322-41524476	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:41522897..41527944-chr15:41573906..41578128,9	K562	blood:
2	chr15:41512004..41513942-chr15:41524174..41526665,2	K562	blood:
3	chr15:41407358..41408983-chr15:41521863..41524451,3	MCF-7	breast:
4	chr15:41220353..41222997-chr15:41522209..41524671,3	K562	blood:
5	chr15:41408234..41410047-chr15:41521744..41524372,2	MCF-7	breast:
6	chr15:41219463..41223303-chr15:41521190..41526712,8	K562	blood:
7	chr15:41406937..41409542-chr15:41521164..41524731,5	K562	blood:
8	chr15:41523711..41525323-chr15:41548065..41550869,2	K562	blood:
9	chr15:41523511..41525481-chr15:41526363..41527921,2	K562	blood:
10	chr15:41522629..41527275-chr15:41575215..41577611,6	K562	blood:
11	chr15:41523451..41525633-chr15:41623235..41625068,3	K562	blood:
12	chr15:41407188..41409566-chr15:41523202..41527124,5	K562	blood:
13	chr15:41307193..41310035-chr15:41522192..41524733,2	MCF-7	breast:

No data

Variant related genes	Relation type
EXD1	TF binding region
ENSG00000104147	Chromatin interaction
ENSG00000128917	Chromatin interaction
ENSG00000187446	Chromatin interaction
ENSG00000247556	Chromatin interaction
ENSG00000128908	Chromatin interaction
ENSG00000137804	Chromatin interaction
ENSG00000259521	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10152855	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070321	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11070325	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11070326	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11855102	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11858115	0.83[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs11858678	0.94[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs12324159	0.83[ASN][1000 genomes]
rs1659227	0.83[ASN][1000 genomes]
rs16971693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16971700	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1717198	0.83[ASN][1000 genomes]
rs1965139	0.83[ASN][1000 genomes]
rs1965140	0.83[ASN][1000 genomes]
rs1971131	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2083239	0.91[ASN][1000 genomes]
rs2164996	0.82[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2578655	0.81[ASN][1000 genomes]
rs28409265	0.85[ASN][1000 genomes]
rs28493237	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28495204	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28568756	0.85[ASN][1000 genomes]
rs28615543	0.83[ASN][1000 genomes]
rs28665387	0.86[ASN][1000 genomes]
rs28735224	0.85[ASN][1000 genomes]
rs2899013	0.88[ASN][1000 genomes]
rs2918462	0.94[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap]
rs2928141	0.83[ASN][1000 genomes]
rs41442144	0.97[GIH][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4258585	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4419033	0.80[ASN][1000 genomes]
rs4445868	0.89[ASN][1000 genomes]
rs537244	0.85[ASN][1000 genomes]
rs551482	0.85[ASN][1000 genomes]
rs55756301	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56082289	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56837771	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57943533	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58083671	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58644012	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59389433	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59616518	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59691280	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60249025	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60422198	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61495227	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61586152	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6492988	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6492991	0.93[ASN][1000 genomes]
rs6492992	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6492993	0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6492994	0.89[ASN][1000 genomes]
rs6492997	0.83[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs66471237	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66510055	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66602495	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67531333	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs68133575	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs690733	0.94[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs691702	0.85[ASN][1000 genomes]
rs7162443	0.86[ASN][1000 genomes]
rs7162503	0.83[ASN][1000 genomes]
rs7165931	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7166205	0.95[ASN][1000 genomes]
rs7166556	0.81[GIH][hapmap]
rs7166905	0.93[ASN][1000 genomes]
rs7167813	0.85[ASN][1000 genomes]
rs7170049	0.94[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs7170913	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7173086	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7175912	0.83[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7178840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7179231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7179676	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7179969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72737765	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73396329	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73396336	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73396340	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8023638	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8026858	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8029792	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8032589	0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8035252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8037302	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8038834	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8039014	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs8039915	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8039934	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8043253	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs909023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs909024	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909025	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9972345	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9972349	0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs9972622	0.88[ASN][1000 genomes]
rs9972623	0.88[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	nsv457120	chr15:41410705-41546631	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv569231	chr15:41410705-41546631	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	esv1844058	chr15:41511916-41548948	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1866400	ZFYVE19	cis	cerebellum	SCAN
rs1866400	CHP	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41522000-41524400	Active TSS	Fetal Kidney	kidney
2	chr15:41522400-41524600	Active TSS	Adipose Nuclei	Adipose
3	chr15:41522600-41524400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr15:41522600-41524400	Active TSS	H1 Cell Line	embryonic stem cell
5	chr15:41522600-41524400	Active TSS	H9 Cell Line	embryonic stem cell
6	chr15:41522600-41524400	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr15:41522600-41524400	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr15:41522600-41524400	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr15:41522600-41524400	Active TSS	Brain Cingulate Gyrus	brain
10	chr15:41522600-41524400	Active TSS	Brain Substantia Nigra	brain
11	chr15:41522600-41524400	Active TSS	Left Ventricle	heart
12	chr15:41522600-41524400	Active TSS	Ovary	ovary
13	chr15:41522600-41524600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:41522600-41524600	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr15:41522600-41524600	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr15:41522600-41524600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:41522600-41524600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:41522600-41524600	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr15:41522600-41524600	Active TSS	Rectal Smooth Muscle	rectum
20	chr15:41522600-41524800	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr15:41522600-41524800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:41522600-41524800	Active TSS	Duodenum Mucosa	Duodenum
23	chr15:41522600-41524800	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr15:41522600-41524800	Active TSS	Rectal Mucosa Donor 31	rectum
25	chr15:41522600-41524800	Active TSS	Right Atrium	heart
26	chr15:41522600-41524800	Active TSS	A549	lung
27	chr15:41522600-41524800	Active TSS	HSMM	muscle
28	chr15:41522600-41524800	Active TSS	NHDF-Ad	bronchial
29	chr15:41522600-41525000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:41522600-41525200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr15:41522600-41525200	Active TSS	Colonic Mucosa	Colon
32	chr15:41522600-41525400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr15:41522800-41524400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr15:41522800-41524400	Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr15:41522800-41524400	Flanking Active TSS	Dnd41	blood
36	chr15:41522800-41524400	Active TSS	HSMMtube	muscle
37	chr15:41522800-41524600	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr15:41522800-41524600	Active TSS	Psoas Muscle	Psoas
39	chr15:41522800-41524600	Active TSS	Right Ventricle	heart
40	chr15:41522800-41524600	Active TSS	Stomach Smooth Muscle	stomach
41	chr15:41522800-41524600	Active TSS	NHLF	lung
42	chr15:41522800-41524800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr15:41522800-41524800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr15:41522800-41524800	Active TSS	Gastric	stomach
45	chr15:41522800-41524800	Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr15:41522800-41525400	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr15:41523000-41524400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:41523000-41524400	Active TSS	Fetal Intestine Small	intestine
49	chr15:41523000-41524600	Active TSS	Fetal Intestine Large	intestine
50	chr15:41523000-41524800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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