Variant report

Variant	rs10438294
Chromosome Location	chr15:73576653-73576654
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:100)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:100 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr15:73576435-73576769	K562	blood:	n/a	n/a
2	CTCF	chr15:73576540-73576690	AoAF	blood vessel:	n/a	n/a
3	CTCF	chr15:73576490-73576702	K562	blood:	n/a	n/a
4	CTCF	chr15:73576501-73576659	HepG2	liver:	n/a	n/a
5	CTCF	chr15:73576580-73576730	HVMF	connective:	n/a	n/a
6	CTCF	chr15:73576520-73576670	GM12868	blood:	n/a	n/a
7	CTCF	chr15:73576473-73576704	SK-N-SH_RA	brain:	n/a	n/a
8	CTCF	chr15:73576540-73576679	GM10248	blood:	n/a	n/a
9	CTCF	chr15:73576520-73576670	HCPEpiC	choroid plexus:	n/a	n/a
10	RAD21	chr15:73576441-73576796	IMR90	lung:	n/a	n/a
11	CTCF	chr15:73576507-73576703	GM12878	blood:	n/a	n/a
12	CTCF	chr15:73576513-73576690	Hela-S3	cervix:	n/a	n/a
13	SMC3	chr15:73576279-73577001	SK-N-SH	brain:	n/a	n/a
14	CTCF	chr15:73576540-73576690	K562	blood:	n/a	n/a
15	CTCF	chr15:73576551-73576685	MCF-7	breast:	n/a	n/a
16	RAD21	chr15:73576339-73576899	A549	lung:	n/a	n/a
17	RAD21	chr15:73576406-73576829	ECC-1	luminal epithelium:	n/a	n/a
18	CTCF	chr15:73576486-73576701	HUVEC	blood vessel:	n/a	n/a
19	CTCF	chr15:73576468-73576697	K562	blood:	n/a	n/a
20	RAD21	chr15:73576312-73576932	HCT-116	colon:	n/a	n/a
21	CTCF	chr15:73575913-73576853	A549	lung:	n/a	n/a
22	SMC3	chr15:73576484-73576770	GM12878	blood:	n/a	n/a
23	CTCF	chr15:73576540-73576690	HCPEpiC	choroid plexus:	n/a	n/a
24	RAD21	chr15:73576450-73576771	GM12878	blood:	n/a	n/a
25	CTCF	chr15:73576520-73576670	GM12878	blood:	n/a	n/a
26	RAD21	chr15:73576301-73576770	MCF-7	breast:	n/a	n/a
27	CTCF	chr15:73576540-73576690	HPAF	blood vessel:	n/a	n/a
28	RAD21	chr15:73576533-73576702	K562	blood:	n/a	n/a
29	CTCF	chr15:73576560-73576710	AG10803	skin:	n/a	n/a
30	CTCF	chr15:73576520-73576670	GM12864	blood:	n/a	n/a
31	CTCF	chr15:73576520-73576670	AG09319	gingival:	n/a	n/a
32	CTCF	chr15:73576511-73576676	SK-N-SH_RA	brain:	n/a	n/a
33	CTCF	chr15:73576540-73576690	AG04449	skin:	n/a	n/a
34	RAD21	chr15:73576429-73576821	Hela-S3	cervix:	n/a	n/a
35	CTCF	chr15:73576580-73576730	NHLF	lung:	n/a	n/a
36	RAD21	chr15:73576361-73576811	ECC-1	luminal epithelium:	n/a	n/a
37	RAD21	chr15:73576449-73576747	HepG2	liver:	n/a	n/a
38	CTCF	chr15:73576560-73576710	GM12874	blood:	n/a	n/a
39	CTCF	chr15:73576520-73576670	GM12873	blood:	n/a	n/a
40	EP300	chr15:73575868-73577099	SK-N-SH	brain:	n/a	chr15:73576803-73576817
41	CTCF	chr15:73576540-73576690	SK-N-SH_RA	brain:	n/a	n/a
42	CTCF	chr15:73576520-73576670	AG09309	skin:	n/a	n/a
43	CTCF	chr15:73576515-73576663	GM10266	blood:	n/a	n/a
44	CTCF	chr15:73576560-73576710	HMEC	breast:	n/a	n/a
45	CTCF	chr15:73575833-73576965	SK-N-SH	brain:	n/a	n/a
46	CTCF	chr15:73576427-73576695	A549	lung:	n/a	n/a
47	CTCF	chr15:73576520-73576670	BJ	skin:	n/a	n/a
48	RAD21	chr15:73576523-73576735	H1-hESC	embryonic stem cell:	n/a	n/a
49	RAD21	chr15:73576380-73576844	MCF-7	breast:	n/a	n/a
50	RAD21	chr15:73576446-73576786	SK-N-SH_RA	brain:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73576151..73576705-chr15:73996872..73997670,2	K562	blood:
2	chr15:73574275..73576773-chr15:73579460..73581037,2	MCF-7	breast:

No data

Variant related genes	Relation type
NEO1	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10048053	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1023924	0.81[CHB][hapmap];0.94[CHD][hapmap]
rs10467949	0.81[ASW][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.88[LWK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap]
rs11072406	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11072409	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1131854	0.92[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11633469	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11636241	0.92[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11639213	0.92[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12050774	0.81[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap]
rs12050848	0.91[CEU][hapmap];0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12708506	0.92[CEU][hapmap];0.88[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12902768	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12907139	0.92[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1479338	0.82[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap]
rs1479339	0.81[CHB][hapmap]
rs1479340	0.81[CHD][hapmap]
rs1564345	0.81[CHD][hapmap]
rs17762600	0.81[CHB][hapmap];0.94[CHD][hapmap];0.80[JPT][hapmap]
rs17829830	0.81[CHB][hapmap];0.94[CHD][hapmap];0.80[JPT][hapmap]
rs17829957	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs1812835	0.85[CEU][hapmap]
rs1871385	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2046017	0.92[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2127277	0.80[CHD][hapmap]
rs2194924	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2251205	0.88[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2252725	0.83[MEX][hapmap];0.83[TSI][hapmap]
rs2415147	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2415148	0.81[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs34013312	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35450875	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3736510	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3743489	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784793	0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3784796	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3784801	0.81[CHB][hapmap]
rs4381562	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4776630	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4777589	0.81[CHD][hapmap];0.84[GIH][hapmap]
rs4777590	0.94[CHD][hapmap]
rs489531	0.83[MEX][hapmap];0.83[TSI][hapmap]
rs56157337	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62015500	0.95[ASN][1000 genomes]
rs62015502	0.82[ASN][1000 genomes]
rs62017779	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7172021	0.81[CHD][hapmap]
rs7175329	0.81[CHD][hapmap];0.89[GIH][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap]
rs747872	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs747873	0.91[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8024575	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8027588	0.92[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8029106	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8035063	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8035925	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8040516	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042700	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs922516	0.81[CHD][hapmap];0.84[GIH][hapmap]
rs9672588	0.92[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9920186	0.87[GIH][hapmap]
rs9972523	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10438294	CYP1A2	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73520600-73579600	Weak transcription	Colon Smooth Muscle	Colon
2	chr15:73527000-73579400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:73535200-73588000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:73536200-73602000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:73538000-73593400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:73540000-73584800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:73544400-73583000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:73546800-73583000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr15:73546800-73588600	Weak transcription	Spleen	Spleen
10	chr15:73547800-73584600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr15:73550800-73581400	Weak transcription	HMEC	breast
12	chr15:73552000-73577800	Weak transcription	Psoas Muscle	Psoas
13	chr15:73552400-73588200	Weak transcription	Hela-S3	cervix
14	chr15:73552800-73598400	Weak transcription	Small Intestine	intestine
15	chr15:73553800-73581200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr15:73560800-73597200	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr15:73562800-73583000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:73563200-73578000	Weak transcription	Aorta	Aorta
19	chr15:73563200-73578800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:73563200-73598600	Weak transcription	Stomach Mucosa	stomach
21	chr15:73563400-73581000	Weak transcription	Fetal Brain Male	brain
22	chr15:73563400-73581200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr15:73563400-73585600	Strong transcription	Fetal Intestine Large	intestine
24	chr15:73563600-73578800	Weak transcription	A549	lung
25	chr15:73563600-73593600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:73566400-73597800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:73568600-73600800	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr15:73569800-73577200	Strong transcription	Brain Hippocampus Middle	brain
29	chr15:73570200-73597000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:73570400-73597000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:73571200-73577800	Weak transcription	Fetal Kidney	kidney
32	chr15:73571200-73601400	Strong transcription	Fetal Stomach	stomach
33	chr15:73572400-73587600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr15:73573200-73578000	Weak transcription	Fetal Lung	lung
35	chr15:73574000-73576800	Strong transcription	Liver	Liver
36	chr15:73574000-73583600	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr15:73574000-73596800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr15:73574200-73577000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr15:73574200-73577000	Strong transcription	Duodenum Mucosa	Duodenum
40	chr15:73574400-73577000	Enhancers	Fetal Heart	heart
41	chr15:73574400-73580000	Strong transcription	Brain Angular Gyrus	brain
42	chr15:73574600-73581200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr15:73574800-73576800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr15:73574800-73588000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:73575000-73577200	Strong transcription	Fetal Muscle Trunk	muscle
46	chr15:73575000-73580200	Strong transcription	Fetal Intestine Small	intestine
47	chr15:73575000-73583600	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr15:73575000-73584200	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr15:73575200-73577000	Enhancers	HSMMtube	muscle
50	chr15:73575200-73583600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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