Variant report

Variant	rs260114
Chromosome Location	chr15:99684105-99684106
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	STAT3	chr15:99683954-99684283	MCF10A-Er-Src	breast:	n/a	n/a
2	RFX5	chr15:99683893-99684227	HepG2	liver:	n/a	chr15:99684179-99684187
3	CEBPB	chr15:99683920-99684196	H1-hESC	embryonic stem cell:	n/a	chr15:99684036-99684047
4	CEBPB	chr15:99683891-99684117	HepG2	liver:	n/a	chr15:99684036-99684047
5	MYC	chr15:99683888-99684209	MCF10A-Er-Src	breast:	n/a	n/a
6	E2F4	chr15:99683941-99684141	MCF10A-Er-Src	breast:	n/a	n/a
7	EP300	chr15:99683999-99684207	HepG2	liver:	n/a	n/a
8	CEBPB	chr15:99683803-99684185	HepG2	liver:	n/a	chr15:99684036-99684047
9	MYC	chr15:99683945-99684339	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr15:99683888-99684337	MCF10A-Er-Src	breast:	n/a	chr15:99684306-99684318
11	STAT3	chr15:99683954-99684263	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr15:99684046-99684441	A549	lung:	n/a	n/a
13	FOXA2	chr15:99683911-99684171	HepG2	liver:	n/a	n/a
14	CEBPD	chr15:99683953-99684144	HepG2	liver:	n/a	n/a
15	FOS	chr15:99683888-99684310	MCF10A-Er-Src	breast:	n/a	n/a
16	CEBPB	chr15:99683859-99684222	HepG2	liver:	n/a	chr15:99684036-99684047
17	POLR2A	chr15:99683936-99684170	MCF10A-Er-Src	breast:	n/a	n/a
18	STAT3	chr15:99683943-99684308	MCF10A-Er-Src	breast:	n/a	n/a
19	FOXA1	chr15:99683833-99684149	HepG2	liver:	n/a	n/a
20	FOXA1	chr15:99683859-99684147	HepG2	liver:	n/a	n/a
21	STAT3	chr15:99683984-99684408	MCF10A-Er-Src	breast:	n/a	n/a
22	CEBPB	chr15:99683885-99684220	HepG2	liver:	n/a	chr15:99684036-99684047
23	FOS	chr15:99683882-99684335	MCF10A-Er-Src	breast:	n/a	chr15:99684306-99684318
24	FOXA1	chr15:99683888-99684130	T-47D	breast:	n/a	n/a
25	FOS	chr15:99683927-99684300	MCF10A-Er-Src	breast:	n/a	n/a
26	FOXA1	chr15:99683889-99684225	HepG2	liver:	n/a	n/a
27	CEBPB	chr15:99683874-99684211	IMR90	lung:	n/a	chr15:99684036-99684047

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:99679173..99681039-chr15:99683301..99685426,2	K562	blood:

Variant related genes	Relation type
TTC23	TF binding region
ENSG00000261616	Chromatin interaction
ENSG00000103852	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12148328	0.81[ASN][1000 genomes]
rs12441651	0.88[ASN][1000 genomes]
rs12915090	1.00[ASW][hapmap];0.84[YRI][hapmap]
rs1670213	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1670216	1.00[CEU][hapmap]
rs1670224	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1670230	0.95[CEU][hapmap]
rs1670232	0.87[ASN][1000 genomes]
rs1670233	0.88[ASN][1000 genomes]
rs1670234	0.88[ASN][1000 genomes]
rs1670244	0.86[ASN][1000 genomes]
rs1670251	0.84[ASN][1000 genomes]
rs1670253	0.81[ASN][1000 genomes]
rs1670254	0.82[ASN][1000 genomes]
rs1703762	1.00[CEU][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs1703766	1.00[CEU][hapmap]
rs1703771	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs187755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs260087	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2602016	0.95[CEU][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2602018	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2602020	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2602021	1.00[ASW][hapmap]
rs2602025	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2602026	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2602031	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2602036	1.00[ASW][hapmap]
rs2602038	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2623184	0.89[ASW][hapmap]
rs2623185	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2623188	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2623189	0.84[AMR][1000 genomes]
rs2623190	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2623191	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2654967	0.82[ASN][1000 genomes]
rs2924346	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3210942	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3743248	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4602019	0.81[CEU][hapmap]
rs4965217	1.00[CEU][hapmap];0.89[GIH][hapmap];0.81[MEX][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6598224	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7163625	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7183226	1.00[ASW][hapmap]
rs921578	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv533375	chr15:99443534-99696221	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1050982	chr15:99450004-99725825	Enhancers Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv530685	chr15:99452377-99713365	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1038870	chr15:99510479-99768374	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh 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	45 gene(s)	inside rSNPs	diseases
11	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
12	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
13	nsv1051782	chr15:99621061-99792967	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
14	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
16	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
17	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs260114	TTC23	cis	parietal	SCAN
rs260114	TTC23	cis	cerebellum	SCAN
rs260114	SYNM	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99664800-99688600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr15:99665000-99714200	Weak transcription	NHEK	skin
3	chr15:99665200-99687800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:99666200-99684200	Weak transcription	HSMMtube	muscle
5	chr15:99673200-99789400	Weak transcription	Small Intestine	intestine
6	chr15:99674400-99704200	Weak transcription	Fetal Kidney	kidney
7	chr15:99676200-99688800	Weak transcription	Brain Angular Gyrus	brain
8	chr15:99676200-99689000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr15:99676200-99691000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr15:99676200-99696200	Weak transcription	NH-A	brain
11	chr15:99676200-99703400	Weak transcription	GM12878-XiMat	blood
12	chr15:99676400-99688600	Weak transcription	Fetal Heart	heart
13	chr15:99676400-99690200	Weak transcription	HSMM	muscle
14	chr15:99676800-99694400	Weak transcription	HUVEC	blood vessel
15	chr15:99677600-99695200	Weak transcription	Hela-S3	cervix
16	chr15:99677800-99696200	Weak transcription	HMEC	breast
17	chr15:99678000-99687800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr15:99678200-99689000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr15:99678200-99696400	Weak transcription	Placenta	Placenta
20	chr15:99678200-99708800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr15:99678400-99689200	Weak transcription	Right Ventricle	heart
22	chr15:99679400-99689600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr15:99679600-99688600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:99679600-99689200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr15:99679800-99684800	Weak transcription	Fetal Muscle Leg	muscle
26	chr15:99679800-99685400	Weak transcription	Gastric	stomach
27	chr15:99679800-99685800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr15:99679800-99687800	Weak transcription	Dnd41	blood
29	chr15:99679800-99688800	Weak transcription	Fetal Intestine Large	intestine
30	chr15:99679800-99689000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:99679800-99689000	Weak transcription	Brain Anterior Caudate	brain
32	chr15:99679800-99689200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr15:99679800-99689200	Weak transcription	Spleen	Spleen
34	chr15:99679800-99689200	Weak transcription	A549	lung
35	chr15:99679800-99696200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:99679800-99696200	Weak transcription	Esophagus	oesophagus
37	chr15:99680200-99687800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr15:99681800-99684400	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr15:99681800-99685000	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr15:99681800-99690200	Enhancers	Colon Smooth Muscle	Colon
41	chr15:99682000-99684400	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr15:99682000-99684400	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr15:99682000-99685200	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr15:99682200-99684200	Enhancers	H1 Cell Line	embryonic stem cell
45	chr15:99682200-99684600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr15:99682200-99684600	Enhancers	H9 Cell Line	embryonic stem cell
47	chr15:99682200-99684600	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr15:99682200-99684600	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr15:99682200-99684600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr15:99682200-99684600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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