Variant report

Variant	rs11854052
Chromosome Location	chr15:59467053-59467054
allele	C/T
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	CTCF	chr15:59467040-59467190	WI-38	lung:	n/a	n/a
2	SIN3A	chr15:59467047-59467391	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr15:59466648-59467356	GM12891	blood:	n/a	n/a
4	CTCF	chr15:59466982-59467476	MCF-7	breast:	n/a	n/a
5	YY1	chr15:59467017-59467366	GM12878	blood:	n/a	chr15:59467119-59467129 chr15:59467118-59467130
6	RAD21	chr15:59466988-59467447	SK-N-SH_RA	brain:	n/a	n/a
7	CTCF	chr15:59466944-59467386	MCF-7	breast:	n/a	n/a
8	RAD21	chr15:59467051-59467413	HepG2	liver:	n/a	n/a
9	POLR2A	chr15:59466798-59467113	GM12878	blood:	n/a	n/a
10	CEBPB	chr15:59467014-59467418	MCF-7	breast:	n/a	n/a
11	RAD21	chr15:59466900-59467531	A549	lung:	n/a	n/a
12	JUND	chr15:59467026-59467281	K562	blood:	n/a	n/a
13	MAX	chr15:59466968-59467849	A549	lung:	n/a	n/a
14	CTCF	chr15:59466942-59467468	A549	lung:	n/a	n/a
15	RAD21	chr15:59466923-59467496	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr15:59466825-59467442	GM12878	blood:	n/a	n/a
17	CREB1	chr15:59467008-59467374	A549	lung:	n/a	n/a
18	EP300	chr15:59467017-59467306	SK-N-SH_RA	brain:	n/a	n/a
19	YY1	chr15:59466958-59467261	K562	blood:	n/a	chr15:59467119-59467129 chr15:59467118-59467130
20	CTCF	chr15:59466995-59467429	H1-hESC	embryonic stem cell:	n/a	n/a
21	YY1	chr15:59466961-59467331	H1-hESC	embryonic stem cell:	n/a	chr15:59467119-59467129 chr15:59467118-59467130
22	SMC3	chr15:59467023-59467403	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr15:59467020-59467170	NHDF-neo	bronchial:	n/a	n/a
24	CTCF	chr15:59467040-59467190	HFF-Myc	foreskin:	n/a	n/a
25	POLR2A	chr15:59466457-59467517	GM12892	blood:	n/a	n/a
26	RAD21	chr15:59466827-59467688	HCT-116	colon:	n/a	n/a
27	CTCF	chr15:59467048-59467422	K562	blood:	n/a	n/a
28	CTCF	chr15:59467029-59467398	GM12878	blood:	n/a	n/a
29	RAD21	chr15:59467052-59467297	K562	blood:	n/a	n/a
30	YY1	chr15:59466951-59467309	A549	lung:	n/a	chr15:59467119-59467129 chr15:59467118-59467130
31	CEBPB	chr15:59467044-59467322	K562	blood:	n/a	n/a
32	RAD21	chr15:59467023-59467366	SK-N-SH_RA	brain:	n/a	n/a
33	POLR2A	chr15:59466618-59467148	Hela-S3	cervix:	n/a	n/a
34	RAD21	chr15:59466938-59467637	HCT-116	colon:	n/a	n/a
35	RAD21	chr15:59466871-59467636	A549	lung:	n/a	n/a
36	FOSL2	chr15:59466951-59468176	A549	lung:	n/a	chr15:59467970-59467978
37	RAD21	chr15:59466880-59467545	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr15:59466654-59467393	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr15:59466775-59467901	SK-N-SH	brain:	n/a	n/a
40	YY1	chr15:59467039-59467299	HCT-116	colon:	n/a	chr15:59467119-59467129 chr15:59467118-59467130
41	CTCF	chr15:59467023-59467369	ECC-1	luminal epithelium:	n/a	n/a
42	YY1	chr15:59466966-59467215	K562	blood:	n/a	chr15:59467119-59467129 chr15:59467118-59467130
43	POLR2A	chr15:59466550-59467264	Hela-S3	cervix:	n/a	n/a
44	CTCF	chr15:59465597-59468147	A549	lung:	n/a	n/a
45	ZNF143	chr15:59466983-59467399	H1-hESC	embryonic stem cell:	n/a	n/a
46	TCF12	chr15:59466836-59467851	A549	lung:	n/a	n/a
47	CTCF	chr15:59466933-59467548	HCT-116	colon:	n/a	n/a
48	CTCF	chr15:59467043-59467344	Medullo	brain:	n/a	n/a
49	NFYA	chr15:59467019-59467334	K562	blood:	n/a	n/a
50	ZNF143	chr15:59467047-59467388	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:59464898..59467094-chr15:59764802..59766481,2	K562	blood:
2	chr15:59466933..59467671-chr15:59784749..59785326,2	K562	blood:
3	chr15:59466810..59467651-chr15:59784616..59785747,3	MCF-7	breast:
4	chr15:59453187..59454025-chr15:59467029..59467674,2	MCF-7	breast:
5	chr15:59466869..59467465-chr15:59704534..59705044,2	MCF-7	breast:
6	chr15:59466796..59467707-chr15:59784788..59785390,2	MCF-7	breast:

Variant related genes	Relation type
MIR2116	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11852281	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854099	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857218	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858347	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442723	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs12916831	0.88[ASN][1000 genomes]
rs16941111	0.80[AFR][1000 genomes]
rs17190785	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17269517	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1872742	0.88[ASN][1000 genomes]
rs2087123	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2101394	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2306790	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58124311	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7165444	0.86[ASN][1000 genomes]
rs7182408	0.93[ASN][1000 genomes]
rs8040100	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923242	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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv833025	chr15:59336148-59522176	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1035868	chr15:59402426-59530594	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59431800-59467200	Weak transcription	Fetal Brain Female	brain
2	chr15:59436000-59473000	Weak transcription	Brain Germinal Matrix	brain
3	chr15:59437800-59484400	Weak transcription	Fetal Brain Male	brain
4	chr15:59445600-59479600	Weak transcription	Fetal Kidney	kidney
5	chr15:59451200-59473600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:59451400-59470400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr15:59451600-59474600	Weak transcription	Psoas Muscle	Psoas
8	chr15:59453400-59467200	Weak transcription	Colon Smooth Muscle	Colon
9	chr15:59453800-59470000	Weak transcription	Right Ventricle	heart
10	chr15:59454000-59482000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr15:59454800-59471600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:59455200-59467200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:59458000-59470000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr15:59458600-59473800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr15:59461000-59474800	Strong transcription	Liver	Liver
16	chr15:59461800-59467200	Strong transcription	Hela-S3	cervix
17	chr15:59462000-59467200	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr15:59462400-59467200	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr15:59463200-59468800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:59463200-59473000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr15:59463400-59468600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr15:59463600-59468600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:59463600-59469000	Weak transcription	Colonic Mucosa	Colon
24	chr15:59463600-59470200	Weak transcription	Esophagus	oesophagus
25	chr15:59463600-59471800	Weak transcription	Small Intestine	intestine
26	chr15:59463800-59470200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr15:59464000-59469600	Weak transcription	Spleen	Spleen
28	chr15:59464000-59472800	Weak transcription	Ovary	ovary
29	chr15:59464200-59467600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr15:59464200-59469600	Weak transcription	Gastric	stomach
31	chr15:59464200-59470000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr15:59464200-59470400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr15:59464200-59470800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr15:59464200-59471600	Weak transcription	Pancreas	Pancrea
35	chr15:59464200-59474000	Weak transcription	HepG2	liver
36	chr15:59464400-59496800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr15:59464600-59468600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:59464800-59467400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:59464800-59467600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr15:59464800-59467600	Strong transcription	HMEC	breast
41	chr15:59465400-59467200	Weak transcription	Fetal Stomach	stomach
42	chr15:59465400-59469000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr15:59465800-59468800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr15:59466000-59467200	Genic enhancers	HUVEC	blood vessel
45	chr15:59466000-59469200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr15:59466200-59468800	Weak transcription	Left Ventricle	heart
47	chr15:59466200-59469000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr15:59466200-59469000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr15:59466200-59469400	Strong transcription	GM12878-XiMat	blood
50	chr15:59466200-59469800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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