Variant report

Variant	rs16973349
Chromosome Location	chr15:42840869-42840870
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:42840396-42841431	Gliobla	brain:	n/a	n/a
2	ATF3	chr15:42840802-42841268	K562	blood:	n/a	chr15:42840988-42840998 chr15:42840991-42840998 chr15:42840987-42841000 chr15:42840990-42841010 chr15:42840991-42841001 chr15:42840988-42841001 chr15:42840989-42841000 chr15:42840988-42841001 chr15:42840991-42841001 chr15:42840990-42840998 chr15:42840988-42840998 chr15:42840991-42841002 chr15:42840991-42840999 chr15:42840987-42841002 chr15:42840990-42841001
3	SIN3AK20	chr15:42840583-42841454	HCT-116	colon:	n/a	n/a
4	JUND	chr15:42840751-42841255	A549	lung:	n/a	chr15:42840990-42840999
5	MYC	chr15:42840386-42841578	K562	blood:	n/a	n/a
6	RAD21	chr15:42840631-42841133	SK-N-SH_RA	brain:	n/a	chr15:42840834-42840847
7	CEBPB	chr15:42840810-42841566	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr15:42840602-42841501	PANC-1	pancreas:	n/a	n/a
9	CHD2	chr15:42840836-42841266	GM12878	blood:	n/a	n/a
10	POLR2A	chr15:42840280-42841567	GM12878	blood:	n/a	n/a
11	MXI1	chr15:42840418-42841385	HepG2	liver:	n/a	n/a
12	POLR2A	chr15:42840552-42841498	SK-N-MC	brain:	n/a	n/a
13	E2F6	chr15:42840780-42841336	A549	lung:	n/a	chr15:42840991-42841000 chr15:42840989-42840998 chr15:42840973-42840985
14	CEBPD	chr15:42840644-42841320	HepG2	liver:	n/a	n/a
15	POLR2A	chr15:42840345-42841533	HL-60	blood:	n/a	n/a
16	ELF1	chr15:42840275-42841358	GM12878	blood:	n/a	n/a
17	E2F6	chr15:42840861-42841158	K562	blood:	n/a	chr15:42840991-42841000 chr15:42840989-42840998 chr15:42840973-42840985
18	ATF1	chr15:42840394-42841581	K562	blood:	n/a	n/a
19	GATA3	chr15:42840790-42841188	T-47D	breast:	n/a	n/a
20	NFIC	chr15:42840283-42841401	GM12878	blood:	n/a	n/a
21	E2F4	chr15:42840305-42841515	MCF10A-Er-Src	breast:	n/a	chr15:42840991-42841000 chr15:42840974-42840985 chr15:42840989-42840998 chr15:42840491-42840501 chr15:42840973-42840985
22	HCFC1	chr15:42840249-42841589	K562	blood:	n/a	n/a
23	SP1	chr15:42840683-42841252	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr15:42840356-42841623	GM12892	blood:	n/a	n/a
25	TCF12	chr15:42840219-42841619	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr15:42840552-42841527	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr15:42840619-42841672	PFSK-1	brain:	n/a	n/a
28	MYC	chr15:42840861-42841526	H1-hESC	embryonic stem cell:	n/a	n/a
29	RCOR1	chr15:42840825-42841512	K562	blood:	n/a	n/a
30	SP1	chr15:42840751-42841256	A549	lung:	n/a	chr15:42841243-42841253 chr15:42841243-42841253
31	JUND	chr15:42840762-42841199	HepG2	liver:	n/a	chr15:42840990-42840999
32	POLR2A	chr15:42840210-42841800	Hela-S3	cervix:	n/a	n/a
33	SIN3AK20	chr15:42840504-42841441	MCF-7	breast:	n/a	n/a
34	POLR2A	chr15:42840269-42841550	H1-hESC	embryonic stem cell:	n/a	n/a
35	SMC3	chr15:42840192-42841652	Hela-S3	cervix:	n/a	n/a
36	MAFK	chr15:42840865-42841097	HepG2	liver:	n/a	n/a
37	TAF1	chr15:42840862-42841211	GM12878	blood:	n/a	n/a
38	CREB1	chr15:42840721-42841438	ECC-1	luminal epithelium:	n/a	chr15:42840988-42841001 chr15:42840988-42841001
39	JUND	chr15:42840808-42841137	H1-hESC	embryonic stem cell:	n/a	chr15:42840990-42840999
40	POLR2A	chr15:42840738-42841250	HepG2	liver:	n/a	n/a
41	GATA1	chr15:42840433-42842436	PBDE	blood:	n/a	chr15:42841996-42842012 chr15:42841999-42842008 chr15:42842001-42842008 chr15:42842001-42842008 chr15:42841994-42842015 chr15:42842001-42842011 chr15:42842001-42842008
42	POLR2A	chr15:42840691-42841294	HepG2	liver:	n/a	n/a
43	CREB1	chr15:42840178-42841592	GM12878	blood:	n/a	chr15:42840988-42841001 chr15:42840988-42841001
44	MXI1	chr15:42840123-42841496	GM12878	blood:	n/a	n/a
45	ZKSCAN1	chr15:42840674-42841458	Hela-S3	cervix:	n/a	n/a
46	HEY1	chr15:42840673-42841215	K562	blood:	n/a	chr15:42840991-42841000 chr15:42840989-42840998
47	JUN	chr15:42840833-42841177	HepG2	liver:	n/a	chr15:42840989-42841002 chr15:42840990-42840999
48	POLR2A	chr15:42840211-42841615	Hela-S3	cervix:	n/a	n/a
49	MXI1	chr15:42840214-42841571	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr15:42840742-42841563	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:42840671..42841382-chr3:172467770..172468757,2	Hela-S3	cervix:
2	chr15:42786881..42789392-chr15:42840485..42842780,2	K562	blood:
3	chr15:42781742..42786032-chr15:42840388..42842565,4	K562	blood:
4	chr15:42565305..42567163-chr15:42839364..42842481,3	K562	blood:
5	chr15:42840496..42841386-chr17:57696797..57697702,2	Hela-S3	cervix:
6	chr15:42498784..42500561-chr15:42840086..42841928,2	K562	blood:
7	chr15:42840090..42842755-chr15:42865653..42870684,5	K562	blood:
8	chr15:42840458..42841183-chrX:20284781..20285310,2	Hela-S3	cervix:
9	chr15:42838345..42842657-chr15:42865696..42868936,4	MCF-7	breast:
10	chr15:42837304..42838910-chr15:42839465..42842272,2	MCF-7	breast:
11	chr15:42783961..42786032-chr15:42840679..42842565,2	K562	blood:
12	chr15:42840229..42841039-chr20:61273829..61274743,2	Hela-S3	cervix:
13	chr15:42838709..42841070-chr15:42866779..42868984,2	MCF-7	breast:
14	chr15:41522531..41524126-chr15:42840731..42842443,2	K562	blood:

Variant related genes	Relation type
LRRC57	TF binding region
HAUS2	TF binding region
ENSG00000214013	Chromatin interaction
ENSG00000103994	Chromatin interaction
ENSG00000178997	Chromatin interaction
ENSG00000141367	Chromatin interaction
ENSG00000103978	Chromatin interaction
ENSG00000187446	Chromatin interaction
ENSG00000167046	Chromatin interaction
ENSG00000166887	Chromatin interaction
ENSG00000092531	Chromatin interaction
ENSG00000177189	Chromatin interaction
ENSG00000180979	Chromatin interaction
ENSG00000114346	Chromatin interaction
ENSG00000101187	Chromatin interaction
ENSG00000159433	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1044866	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11541527	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36090286	0.85[AFR][1000 genomes]
rs5009460	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57249373	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57349778	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58122107	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs58562675	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58952814	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59058205	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59091063	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60060355	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60168929	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60606292	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60697170	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60839827	1.00[AMR][1000 genomes]
rs61368952	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61474811	0.85[AMR][1000 genomes]
rs6493048	0.92[AFR][1000 genomes]
rs6493049	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6493050	0.95[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7166143	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7166633	0.87[AMR][1000 genomes]
rs7172064	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7172955	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7173155	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7175059	1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs7178822	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7181938	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73402762	0.85[AMR][1000 genomes]
rs73402776	0.85[AMR][1000 genomes]
rs73402796	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73404708	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404711	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404725	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404729	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404744	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404746	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404754	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73404758	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404768	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404774	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404775	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404793	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406526	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406531	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406544	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406553	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406557	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs768118	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8023948	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8027207	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8031383	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8031883	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8033555	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8033810	1.00[AMR][1000 genomes]
rs8034001	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8035877	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8036927	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs8037277	0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8040624	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][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	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 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	chr15:42839400-42842000	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr15:42839400-42842200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:42839600-42842000	Active TSS	Right Ventricle	heart
4	chr15:42839600-42842600	Active TSS	GM12878-XiMat	blood
5	chr15:42839800-42842000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:42839800-42842000	Active TSS	Brain Angular Gyrus	brain
7	chr15:42839800-42842000	Active TSS	Fetal Kidney	kidney
8	chr15:42839800-42842200	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr15:42839800-42842200	Active TSS	A549	lung
10	chr15:42839800-42842400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr15:42839800-42842800	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr15:42840000-42841400	Active TSS	Fetal Stomach	stomach
13	chr15:42840000-42841600	Active TSS	Aorta	Aorta
14	chr15:42840000-42841600	Active TSS	Placenta Amnion	Placenta Amnion
15	chr15:42840000-42841800	Active TSS	Ovary	ovary
16	chr15:42840000-42842000	Active TSS	H9 Cell Line	embryonic stem cell
17	chr15:42840000-42842000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:42840000-42842000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr15:42840000-42842000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr15:42840000-42842000	Active TSS	Fetal Intestine Large	intestine
21	chr15:42840000-42842000	Active TSS	Fetal Intestine Small	intestine
22	chr15:42840000-42842000	Active TSS	NHDF-Ad	bronchial
23	chr15:42840000-42842200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr15:42840000-42842200	Active TSS	Fetal Muscle Trunk	muscle
25	chr15:42840000-42842400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:42840000-42842400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:42840000-42842400	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr15:42840000-42842400	Active TSS	HSMMtube	muscle
29	chr15:42840000-42842600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr15:42840200-42841200	Active TSS	Brain Germinal Matrix	brain
31	chr15:42840200-42841600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr15:42840200-42841600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:42840200-42841600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:42840200-42841600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr15:42840200-42841600	Active TSS	Brain Cingulate Gyrus	brain
36	chr15:42840200-42841600	Active TSS	Colon Smooth Muscle	Colon
37	chr15:42840200-42841600	Active TSS	Fetal Heart	heart
38	chr15:42840200-42841600	Active TSS	Gastric	stomach
39	chr15:42840200-42841600	Active TSS	Left Ventricle	heart
40	chr15:42840200-42841600	Active TSS	Lung	lung
41	chr15:42840200-42841600	Active TSS	Pancreas	Pancrea
42	chr15:42840200-42841600	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr15:42840200-42841600	Active TSS	Small Intestine	intestine
44	chr15:42840200-42841600	Active TSS	Stomach Mucosa	stomach
45	chr15:42840200-42841600	Active TSS	Spleen	Spleen
46	chr15:42840200-42841600	Bivalent/Poised TSS	HepG2	liver
47	chr15:42840200-42841800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:42840200-42841800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr15:42840200-42842000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr15:42840200-42842000	Active TSS	Breast Myoepithelial Primary Cells	Breast

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