Variant report

Variant	rs16861115
Chromosome Location	chr3:113234151-113234152
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	POLR2A	chr3:113233728-113234300	K562	blood:	n/a	n/a
2	PML	chr3:113233718-113234251	MCF-7	breast:	n/a	chr3:113234136-113234144
3	BRCA1	chr3:113233047-113234197	Hela-S3	cervix:	n/a	n/a
4	FOXP2	chr3:113233580-113234172	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr3:113233500-113235394	MCF-7	breast:	n/a	n/a
6	TAF1	chr3:113233808-113234246	PFSK-1	brain:	n/a	n/a
7	NRF1	chr3:113233515-113234277	H1-hESC	embryonic stem cell:	n/a	chr3:113234082-113234096 chr3:113234085-113234096 chr3:113234085-113234094 chr3:113234084-113234095
8	ATF3	chr3:113233781-113234321	A549	lung:	n/a	n/a
9	POLR2A	chr3:113233658-113234437	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:113233580-113234305	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr3:113233495-113234251	HL-60	blood:	n/a	n/a
12	GABPA	chr3:113233352-113234508	MCF-7	breast:	n/a	chr3:113234082-113234096 chr3:113234085-113234096 chr3:113234085-113234094
13	PML	chr3:113233839-113234225	GM12878	blood:	n/a	chr3:113234136-113234144
14	NRF1	chr3:113233476-113234265	Hela-S3	cervix:	n/a	chr3:113234082-113234096 chr3:113234085-113234096 chr3:113234085-113234094 chr3:113234084-113234095
15	PAX5	chr3:113233805-113234171	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:113233575-113234351	K562	blood:	n/a	n/a
17	ZNF384	chr3:113233994-113234975	GM12878	blood:	n/a	n/a
18	YY1	chr3:113233878-113234238	A549	lung:	n/a	chr3:113234079-113234093
19	MAFK	chr3:113233345-113234152	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr3:113233686-113234294	GM12891	blood:	n/a	n/a
21	CREB1	chr3:113233797-113234253	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr3:113233640-113234301	GM12891	blood:	n/a	n/a
23	NRF1	chr3:113233597-113234255	HepG2	liver:	n/a	chr3:113234082-113234096 chr3:113234085-113234096 chr3:113234085-113234094 chr3:113234084-113234095
24	POLR2A	chr3:113233462-113234358	GM12892	blood:	n/a	n/a
25	ELK1	chr3:113233794-113234199	Hela-S3	cervix:	n/a	n/a
26	ELF1	chr3:113233594-113234208	A549	lung:	n/a	chr3:113233947-113233959
27	POLR2A	chr3:113233687-113234417	PANC-1	pancreas:	n/a	n/a
28	GABPA	chr3:113233673-113234246	Hela-S3	cervix:	n/a	chr3:113234082-113234096 chr3:113234085-113234096 chr3:113234085-113234094
29	TCF12	chr3:113233493-113235250	A549	lung:	n/a	chr3:113234598-113234607
30	SP1	chr3:113233468-113234266	A549	lung:	n/a	chr3:113234046-113234055
31	POLR2A	chr3:113233762-113234206	A549	lung:	n/a	n/a
32	GATA3	chr3:113233892-113234227	T-47D	breast:	n/a	n/a
33	POLR2A	chr3:113233484-113234392	Gliobla	brain:	n/a	n/a
34	HA-E2F1	chr3:113233325-113234602	MCF-7	breast:	n/a	chr3:113234086-113234095 chr3:113233801-113233811 chr3:113233764-113233774
35	GABPA	chr3:113233514-113234216	MCF-7	breast:	n/a	chr3:113234082-113234096 chr3:113234085-113234096 chr3:113234085-113234094
36	TAF1	chr3:113233545-113234206	Hela-S3	cervix:	n/a	n/a
37	SMARCB1	chr3:113233437-113234369	Hela-S3	cervix:	n/a	n/a
38	TAF1	chr3:113233805-113234207	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr3:113233054-113235426	HepG2	liver:	n/a	n/a
40	POLR2A	chr3:113233521-113234224	H1-neurons	neurons:	n/a	n/a
41	POLR2A	chr3:113233450-113234332	K562	blood:	n/a	n/a
42	GABPA	chr3:113233538-113234256	SK-N-SH	brain:	n/a	chr3:113234082-113234096 chr3:113234085-113234096 chr3:113234085-113234094
43	MXI1	chr3:113233496-113234223	HepG2	liver:	n/a	chr3:113234028-113234043
44	TAF1	chr3:113233500-113234254	ECC-1	luminal epithelium:	n/a	n/a
45	MAX	chr3:113233535-113234222	A549	lung:	n/a	chr3:113234051-113234060
46	GABPA	chr3:113233482-113234305	A549	lung:	n/a	chr3:113234082-113234096 chr3:113234085-113234096 chr3:113234085-113234094
47	POLR2A	chr3:113233436-113235338	MCF10A-Er-Src	breast:	n/a	n/a
48	TAF1	chr3:113233808-113234303	K562	blood:	n/a	n/a
49	POLR2A	chr3:113233587-113234423	GM12892	blood:	n/a	n/a
50	POLR2A	chr3:113233323-113234413	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:113229615..113239929-chr3:113247196..113257849,45	MCF-7	breast:
2	chr3:112279637..112281423-chr3:113232414..113235211,2	K562	blood:
3	chr3:113232695..113235446-chr3:113249011..113251267,3	K562	blood:
4	chr3:112709917..112711539-chr3:113232036..113234156,2	K562	blood:
5	chr3:113233753..113235613-chr3:113463995..113467002,3	MCF-7	breast:
6	chr3:113232788..113235774-chr3:113464780..113467765,2	MCF-7	breast:

Variant related genes	Relation type
SPICE1	TF binding region
ENSG00000272844	Chromatin interaction
ENSG00000072858	Chromatin interaction
ENSG00000242659	Chromatin interaction
ENSG00000163607	Chromatin interaction
ENSG00000138459	Chromatin interaction
ENSG00000144848	Chromatin interaction
ENSG00000121579	Chromatin interaction
ENSG00000114573	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11917869	1.00[AMR][1000 genomes]
rs11919091	1.00[AMR][1000 genomes]
rs11920233	1.00[AMR][1000 genomes]
rs11920468	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11920635	0.87[YRI][hapmap]
rs11920795	1.00[AMR][1000 genomes]
rs11921249	1.00[AMR][1000 genomes]
rs11922003	1.00[AMR][1000 genomes]
rs11924899	1.00[AMR][1000 genomes]
rs11925633	1.00[AMR][1000 genomes]
rs11926656	1.00[AMR][1000 genomes]
rs11929188	1.00[AMR][1000 genomes]
rs1463639	0.85[YRI][hapmap]
rs16845109	0.85[YRI][hapmap]
rs16845110	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs16860854	1.00[AMR][1000 genomes]
rs16860875	1.00[AMR][1000 genomes]
rs16860995	0.85[YRI][hapmap]
rs16861019	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs16861059	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs2306068	0.87[YRI][hapmap]
rs2306070	0.87[YRI][hapmap]
rs6783691	0.87[YRI][hapmap]
rs7430385	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv877349	chr3:113208224-113323787	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv877350	chr3:113208224-113332235	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 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	chr3:113232400-113235200	Active TSS	A549	lung
2	chr3:113232600-113234400	Active TSS	HMEC	breast
3	chr3:113232600-113234600	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr3:113232600-113234600	Active TSS	GM12878-XiMat	blood
5	chr3:113232600-113234600	Active TSS	K562	blood
6	chr3:113232600-113234600	Active TSS	Osteobl	bone
7	chr3:113232600-113234800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:113232600-113234800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:113232600-113234800	Active TSS	Right Ventricle	heart
10	chr3:113232600-113235000	Active TSS	Thymus	Thymus
11	chr3:113232600-113235000	Active TSS	NHLF	lung
12	chr3:113232800-113234600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:113232800-113234600	Active TSS	Brain Germinal Matrix	brain
14	chr3:113232800-113234600	Active TSS	Fetal Stomach	stomach
15	chr3:113232800-113234800	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr3:113232800-113234800	Active TSS	H1 Cell Line	embryonic stem cell
17	chr3:113232800-113235000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:113232800-113235200	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr3:113233000-113234400	Active TSS	Fetal Thymus	thymus
20	chr3:113233000-113234600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:113233000-113234600	Active TSS	Muscle Satellite Cultured Cells	--
22	chr3:113233000-113234600	Active TSS	Fetal Muscle Trunk	muscle
23	chr3:113233000-113234600	Active TSS	Placenta Amnion	Placenta Amnion
24	chr3:113233000-113234600	Active TSS	Stomach Mucosa	stomach
25	chr3:113233000-113234600	Active TSS	Hela-S3	cervix
26	chr3:113233000-113234600	Active TSS	HSMMtube	muscle
27	chr3:113233000-113234800	Active TSS	H9 Cell Line	embryonic stem cell
28	chr3:113233000-113234800	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr3:113233000-113234800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:113233000-113234800	Active TSS	Fetal Intestine Large	intestine
31	chr3:113233000-113234800	Active TSS	Fetal Intestine Small	intestine
32	chr3:113233000-113234800	Active TSS	Stomach Smooth Muscle	stomach
33	chr3:113233000-113234800	Active TSS	HSMM	muscle
34	chr3:113233000-113234800	Active TSS	NHDF-Ad	bronchial
35	chr3:113233000-113235000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:113233000-113235000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:113233000-113235000	Active TSS	Right Atrium	heart
38	chr3:113233000-113235200	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr3:113233000-113235400	Active TSS	Psoas Muscle	Psoas
40	chr3:113233200-113234400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:113233200-113234400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:113233200-113234400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:113233200-113234400	Active TSS	Gastric	stomach
44	chr3:113233200-113234600	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr3:113233200-113234600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr3:113233200-113234600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr3:113233200-113234600	Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr3:113233200-113234600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:113233200-113234600	Active TSS	Aorta	Aorta
50	chr3:113233200-113234600	Active TSS	Colon Smooth Muscle	Colon

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