Variant report

Variant	rs35123814
Chromosome Location	chr15:41624579-41624580
allele	C/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	RAD21	chr15:41624154-41624725	IMR90	lung:	n/a	chr15:41624358-41624377
2	POLR2A	chr15:41624299-41625433	Gliobla	brain:	n/a	n/a
3	TAF1	chr15:41624205-41625320	PFSK-1	brain:	n/a	n/a
4	SETDB1	chr15:41624479-41625409	U2OS	brain:	n/a	n/a
5	HA-E2F1	chr15:41624464-41625423	Hela-S3	cervix:	n/a	chr15:41624795-41624805 chr15:41625277-41625286 chr15:41624934-41624951 chr15:41624933-41624947 chr15:41624905-41624912 chr15:41624766-41624776 chr15:41624904-41624915 chr15:41624909-41624918
6	NRF1	chr15:41624348-41625415	GM12878	blood:	n/a	chr15:41624908-41624919 chr15:41624907-41624918 chr15:41625277-41625286
7	ZC3H11A	chr15:41624342-41625269	K562	blood:	n/a	n/a
8	RAD21	chr15:41624157-41624582	H1-hESC	embryonic stem cell:	n/a	chr15:41624358-41624377
9	EP300	chr15:41624164-41625632	K562	blood:	n/a	chr15:41625277-41625286
10	SIN3AK20	chr15:41624124-41624824	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr15:41624357-41625641	GM12878	blood:	n/a	n/a
12	SIN3AK20	chr15:41624027-41625733	HCT-116	colon:	n/a	n/a
13	TBP	chr15:41624253-41625773	GM12878	blood:	n/a	n/a
14	CCNT2	chr15:41624308-41625720	K562	blood:	n/a	n/a
15	HDAC2	chr15:41624193-41624862	HepG2	liver:	n/a	n/a
16	POLR2A	chr15:41624151-41625472	K562	blood:	n/a	n/a
17	SIN3AK20	chr15:41623952-41625782	MCF-7	breast:	n/a	n/a
18	POLR2A	chr15:41624299-41625485	K562	blood:	n/a	n/a
19	BHLHE40	chr15:41624338-41625258	K562	blood:	n/a	n/a
20	POLR2A	chr15:41624298-41625587	NB4	blood:	n/a	n/a
21	CTCF	chr15:41624136-41624786	K562	blood:	n/a	chr15:41624348-41624357 chr15:41624362-41624375 chr15:41624360-41624378 chr15:41624362-41624375
22	ZBTB33	chr15:41624529-41625296	HCT-116	colon:	n/a	n/a
23	NR2F2	chr15:41624286-41625798	K562	blood:	n/a	n/a
24	SIN3AK20	chr15:41624188-41624883	K562	blood:	n/a	n/a
25	NRF1	chr15:41624355-41625184	H1-hESC	embryonic stem cell:	n/a	chr15:41624908-41624919 chr15:41624907-41624918
26	ELF1	chr15:41624328-41625571	GM12878	blood:	n/a	n/a
27	POLR2A	chr15:41624124-41625588	K562	blood:	n/a	n/a
28	POLR2A	chr15:41624275-41625438	H1-hESC	embryonic stem cell:	n/a	n/a
29	EP300	chr15:41624391-41625248	HepG2	liver:	n/a	n/a
30	POLR2A	chr15:41624146-41626151	Hela-S3	cervix:	n/a	n/a
31	RAD21	chr15:41624153-41624639	SK-N-SH_RA	brain:	n/a	chr15:41624358-41624377
32	CTCF	chr15:41624277-41624648	GM13977	blood:	n/a	chr15:41624348-41624357 chr15:41624362-41624375 chr15:41624360-41624378 chr15:41624362-41624375
33	TAF7	chr15:41624240-41625476	H1-hESC	embryonic stem cell:	n/a	n/a
34	SP4	chr15:41624256-41624977	H1-hESC	embryonic stem cell:	n/a	chr15:41624796-41624812
35	FOXM1	chr15:41624422-41625826	GM12878	blood:	n/a	n/a
36	JUN	chr15:41624415-41625283	K562	blood:	n/a	n/a
37	CEBPB	chr15:41624239-41625822	Hela-S3	cervix:	n/a	chr15:41625550-41625567 chr15:41624717-41624728
38	TBP	chr15:41624245-41625536	H1-hESC	embryonic stem cell:	n/a	n/a
39	ATF2	chr15:41624260-41625778	GM12878	blood:	n/a	n/a
40	TAF1	chr15:41624294-41625429	GM12878	blood:	n/a	n/a
41	CTCF	chr15:41624262-41624690	H1-hESC	embryonic stem cell:	n/a	chr15:41624348-41624357 chr15:41624362-41624375 chr15:41624360-41624378 chr15:41624362-41624375
42	POLR2A	chr15:41624266-41625550	GM12878	blood:	n/a	n/a
43	MTA3	chr15:41624260-41624863	GM12878	blood:	n/a	n/a
44	PML	chr15:41624221-41625628	K562	blood:	n/a	n/a
45	TCF12	chr15:41624177-41625679	ECC-1	luminal epithelium:	n/a	n/a
46	ZNF143	chr15:41624237-41625226	K562	blood:	n/a	n/a
47	MYC	chr15:41624481-41625407	K562	blood:	n/a	n/a
48	JUND	chr15:41624534-41624940	A549	lung:	n/a	n/a
49	YY1	chr15:41624219-41625234	SK-N-SH_RA	brain:	n/a	n/a
50	TCF12	chr15:41624407-41625603	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:41624281..41625198-chr19:3093881..3094809,2	Hela-S3	cervix:
2	chr15:41523451..41525633-chr15:41623235..41625068,3	K562	blood:
3	chr15:41406745..41409392-chr15:41623521..41626579,5	K562	blood:
4	chr15:41575391..41577503-chr15:41623750..41625308,2	MCF-7	breast:
5	chr15:41624298..41625165-chr19:5790834..5791761,2	NB4	blood:
6	chr15:41624298..41625139-chr16:30388538..30389381,2	NB4	blood:
7	chr15:41573497..41577986-chr15:41624362..41627823,9	K562	blood:
8	chr15:41623748..41626097-chr15:41632335..41635242,3	K562	blood:
9	chr15:41624548..41625512-chr2:88927297..88927982,3	Hela-S3	cervix:
10	chr15:41624471..41625190-chr3:156878541..156879113,2	Hela-S3	cervix:
11	chr15:41624382..41626552-chr15:41708725..41711080,3	K562	blood:
12	chr15:41624332..41625450-chr7:139044081..139045186,3	Hela-S3	cervix:
13	chr15:41624531..41625112-chr5:38556858..38557449,2	Hela-S3	cervix:
14	chr15:41575115..41577125-chr15:41624466..41626801,3	MCF-7	breast:
15	chr15:41621801..41625398-chr15:41692470..41696241,5	K562	blood:
16	chr15:41623948..41624674-chr19:32896567..32897235,2	NB4	blood:
17	chr15:41624254..41626833-chr15:41952098..41954867,2	K562	blood:
18	chr15:41624232..41625170-chr15:65588350..65588963,2	Hela-S3	cervix:
19	chr15:41406809..41409126-chr15:41623521..41625356,3	K562	blood:
20	chr15:41407574..41409310-chr15:41622908..41625714,2	MCF-7	breast:
21	chr15:41575029..41577348-chr15:41624329..41626974,5	K562	blood:
22	chr15:41624460..41625122-chr2:28974191..28974875,2	Hela-S3	cervix:

Variant related genes	Relation type
NUSAP1	TF binding region
ENSG00000137806	Chromatin interaction
ENSG00000247556	Chromatin interaction
ENSG00000146963	Chromatin interaction
ENSG00000213639	Chromatin interaction
ENSG00000137815	Chromatin interaction
ENSG00000163660	Chromatin interaction
ENSG00000234028	Chromatin interaction
ENSG00000128908	Chromatin interaction
ENSG00000187446	Chromatin interaction
ENSG00000141994	Chromatin interaction
ENSG00000244968	Chromatin interaction
ENSG00000178904	Chromatin interaction
ENSG00000174197	Chromatin interaction
ENSG00000137804	Chromatin interaction
ENSG00000180209	Chromatin interaction
ENSG00000199568	Chromatin interaction
ENSG00000088256	Chromatin interaction
ENSG00000273391	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs36124939	0.82[AFR][1000 genomes]
rs55643943	0.80[AFR][1000 genomes]
rs55838056	0.86[AFR][1000 genomes]
rs56140669	0.82[AFR][1000 genomes]
rs58165973	0.98[AFR][1000 genomes]
rs58218403	0.95[AFR][1000 genomes]
rs59034095	0.89[AFR][1000 genomes]
rs59343255	0.98[AFR][1000 genomes]
rs59850482	0.93[AFR][1000 genomes]
rs74012258	0.82[AFR][1000 genomes]
rs74012259	0.98[AFR][1000 genomes]
rs74012263	0.98[AFR][1000 genomes]
rs74012273	0.83[AFR][1000 genomes]
rs74012275	0.84[AFR][1000 genomes]
rs74012276	0.89[AFR][1000 genomes]
rs8025218	0.84[AFR][1000 genomes]
rs8028208	0.89[AFR][1000 genomes]
rs8029815	0.84[AFR][1000 genomes]
rs8035341	0.98[AFR][1000 genomes]
rs8038086	0.82[AFR][1000 genomes]
rs8038185	0.82[AFR][1000 genomes]
rs8039815	0.89[AFR][1000 genomes]
rs8041170	0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044438	chr15:41560160-41745480	Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv1038923	chr15:41585028-41754890	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv1045142	chr15:41585044-41738314	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv977843	chr15:41608625-41625613	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	44 gene(s)	inside rSNPs	diseases
5	nsv1039283	chr15:41620499-41745480	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	63 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	chr15:41623000-41626800	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr15:41623000-41627200	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr15:41623000-41627200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr15:41623000-41627200	Active TSS	A549	lung
5	chr15:41623000-41627400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:41623400-41627000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:41623400-41627200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr15:41623400-41627200	Active TSS	H1 Cell Line	embryonic stem cell
9	chr15:41623400-41627400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr15:41623600-41626800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:41623600-41626800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:41623600-41626800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:41623600-41627000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:41623600-41627000	Active TSS	H9 Cell Line	embryonic stem cell
15	chr15:41623600-41627200	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr15:41623600-41627200	Active TSS	Thymus	Thymus
17	chr15:41623600-41627200	Active TSS	Hela-S3	cervix
18	chr15:41623800-41624600	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr15:41623800-41625400	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr15:41623800-41625400	Active TSS	Fetal Brain Male	brain
21	chr15:41623800-41625800	Active TSS	Fetal Muscle Trunk	muscle
22	chr15:41623800-41626200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:41623800-41626200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr15:41623800-41626400	Active TSS	Osteobl	bone
25	chr15:41623800-41626600	Active TSS	Fetal Thymus	thymus
26	chr15:41623800-41626800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr15:41623800-41627200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr15:41623800-41627200	Active TSS	NHDF-Ad	bronchial
29	chr15:41623800-41627400	Active TSS	GM12878-XiMat	blood
30	chr15:41623800-41627400	Active TSS	K562	blood
31	chr15:41624000-41624600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr15:41624000-41624600	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr15:41624000-41624600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr15:41624000-41624600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr15:41624000-41624600	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr15:41624000-41624800	Flanking Active TSS	Liver	Liver
37	chr15:41624000-41625200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:41624000-41625200	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr15:41624000-41625600	Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr15:41624000-41625600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:41624000-41625600	Active TSS	Psoas Muscle	Psoas
42	chr15:41624000-41625800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr15:41624000-41625800	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr15:41624000-41625800	Active TSS	Ovary	ovary
45	chr15:41624000-41625800	Active TSS	Right Ventricle	heart
46	chr15:41624000-41625800	Bivalent/Poised TSS	HepG2	liver
47	chr15:41624000-41626000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:41624000-41626000	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr15:41624000-41626000	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr15:41624000-41626200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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