Variant report

Variant	rs6768093
Chromosome Location	chr3:142298200-142298201
allele	A/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	MAX	chr3:142296519-142298266	A549	lung:	n/a	n/a
2	SIN3AK20	chr3:142296938-142298318	MCF-7	breast:	n/a	n/a
3	MTA3	chr3:142296982-142298737	GM12878	blood:	n/a	n/a
4	ELF1	chr3:142297158-142298229	SK-N-SH	brain:	n/a	chr3:142297609-142297622 chr3:142297661-142297670
5	MXI1	chr3:142297007-142298484	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:142297265-142298328	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:142296959-142298595	GM18505	blood:	n/a	n/a
8	NFIC	chr3:142296728-142298205	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:142296973-142298242	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:142297125-142298432	GM18951	blood:	n/a	n/a
11	SIN3AK20	chr3:142296994-142298224	HCT-116	colon:	n/a	n/a
12	SP1	chr3:142297166-142298260	A549	lung:	n/a	chr3:142297742-142297751 chr3:142297742-142297752 chr3:142297743-142297752 chr3:142297738-142297752 chr3:142297741-142297753 chr3:142297741-142297753 chr3:142297410-142297419 chr3:142297742-142297752 chr3:142297743-142297752
13	KAP1	chr3:142297289-142298344	U2OS	brain:	n/a	n/a
14	BCLAF1	chr3:142297354-142298206	GM12878	blood:	n/a	chr3:142297368-142297381
15	MAX	chr3:142297176-142298212	K562	blood:	n/a	n/a
16	ATF2	chr3:142297242-142298410	GM12878	blood:	n/a	n/a
17	PML	chr3:142296841-142298327	GM12878	blood:	n/a	n/a
18	YY1	chr3:142297084-142298392	SK-N-SH	brain:	n/a	chr3:142297370-142297381 chr3:142297742-142297751
19	TAF1	chr3:142297017-142298223	ECC-1	luminal epithelium:	n/a	n/a
20	MAX	chr3:142297089-142298237	MCF-7	breast:	n/a	n/a
21	MXI1	chr3:142296408-142298719	SK-N-SH	brain:	n/a	n/a
22	RELA	chr3:142297196-142298280	GM15510	blood:	n/a	n/a
23	POLR2A	chr3:142296667-142298686	GM12891	blood:	n/a	n/a
24	POLR2A	chr3:142296817-142298665	MCF10A-Er-Src	breast:	n/a	n/a
25	GATA3	chr3:142297169-142298204	A549	lung:	n/a	chr3:142298099-142298110
26	CUX1	chr3:142297366-142298226	GM12878	blood:	n/a	n/a
27	ELF1	chr3:142297099-142298250	MCF-7	breast:	n/a	chr3:142297609-142297622 chr3:142297661-142297670
28	POLR2A	chr3:142295895-142298691	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr3:142296847-142298351	IMR90	lung:	n/a	n/a
30	ELF1	chr3:142297116-142298205	HCT-116	colon:	n/a	chr3:142297609-142297622 chr3:142297661-142297670
31	SMC3	chr3:142297819-142298384	HepG2	liver:	n/a	n/a
32	POLR2A	chr3:142296769-142298255	GM12892	blood:	n/a	n/a
33	STAT5A	chr3:142296975-142298434	GM12878	blood:	n/a	chr3:142297093-142297104 chr3:142297123-142297146 chr3:142297411-142297423
34	POLR2A	chr3:142297335-142298314	GM12878	blood:	n/a	n/a
35	MXI1	chr3:142296459-142298498	IMR90	lung:	n/a	n/a
36	MAX	chr3:142296989-142298239	HCT-116	colon:	n/a	n/a
37	POLR2A	chr3:142297141-142298208	HepG2	liver:	n/a	n/a
38	SIN3A	chr3:142297113-142298309	GM12878	blood:	n/a	n/a
39	POLR2A	chr3:142297129-142298265	GM12892	blood:	n/a	n/a
40	POLR2A	chr3:142296864-142298261	SK-N-MC	brain:	n/a	n/a
41	WRNIP1	chr3:142296734-142298222	GM12878	blood:	n/a	n/a
42	MAX	chr3:142297161-142298225	GM12878	blood:	n/a	n/a
43	CUX1	chr3:142297675-142298531	K562	blood:	n/a	n/a
44	MAX	chr3:142296766-142298258	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr3:142297187-142298681	GM12878	blood:	n/a	n/a
46	TCF12	chr3:142296897-142298293	A549	lung:	n/a	chr3:142297402-142297412
47	IRF1	chr3:142297403-142298492	K562	blood:	n/a	chr3:142297834-142297845 chr3:142297741-142297755
48	ZNF143	chr3:142297307-142298200	K562	blood:	n/a	n/a
49	TCF12	chr3:142297094-142298251	ECC-1	luminal epithelium:	n/a	chr3:142297402-142297412
50	ELF1	chr3:142296952-142298232	HCT-116	colon:	n/a	chr3:142297609-142297622 chr3:142297661-142297670

No.	Distal block	Cell Line	Cell type
1	chr3:142297806..142298379-chr5:1524091..1524637,2	NB4	blood:
2	chr3:142297625..142299268-chr3:142441632..142444151,3	K562	blood:
3	chr3:142280626..142282527-chr3:142296623..142299039,2	K562	blood:
4	chr12:46753334..46754030-chr3:142297866..142298600,2	Hela-S3	cervix:
5	chr3:142297403..142299294-chr3:142720282..142722143,3	MCF-7	breast:
6	chr3:142296149..142300233-chr3:142313670..142315817,6	K562	blood:
7	chr3:142297466..142299799-chr3:142313558..142315620,3	K562	blood:
8	chr3:142295918..142298932-chr3:142719049..142722504,4	MCF-7	breast:
9	chr3:142280626..142283157-chr3:142296079..142299039,3	K562	blood:
10	chr3:142297625..142299268-chr3:142441632..142445353,4	K562	blood:
11	chr13:98628143..98628846-chr3:142297511..142298310,2	NB4	blood:
12	chr3:142217843..142219879-chr3:142296547..142298953,2	MCF-7	breast:
13	chr3:142294568..142300006-chr3:142310942..142319455,13	MCF-7	breast:
14	chr3:142296202..142300183-chr3:142719946..142722583,4	K562	blood:
15	chr3:142294183..142301262-chr3:142311308..142318922,13	MCF-7	breast:
16	chr3:142295888..142299099-chr3:142720440..142723490,3	K562	blood:
17	chr3:142297949..142299634-chr3:142710792..142712643,2	MCF-7	breast:
18	chr17:27046573..27047488-chr3:142297296..142298228,2	Hela-S3	cervix:
19	chr3:142296891..142299259-chr3:142680803..142682548,2	K562	blood:

Variant related genes	Relation type
RPL6P9	TF binding region
ATR	TF binding region
ENSG00000188582	Chromatin interaction
ENSG00000198242	Chromatin interaction
ENSG00000065150	Chromatin interaction
ENSG00000163714	Chromatin interaction
ENSG00000175054	Chromatin interaction
ENSG00000153395	Chromatin interaction
ENSG00000144935	Chromatin interaction
ENSG00000268129	Chromatin interaction
ENSG00000241570	Chromatin interaction
ENSG00000120756	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10935465	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1129393	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13065075	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13067795	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13069307	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13085998	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13093869	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13098343	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1357529	0.85[EUR][1000 genomes]
rs1357530	0.86[EUR][1000 genomes]
rs1916639	0.86[EUR][1000 genomes]
rs1983434	0.87[EUR][1000 genomes]
rs1983435	0.87[EUR][1000 genomes]
rs2030613	0.87[EUR][1000 genomes]
rs2049325	0.87[EUR][1000 genomes]
rs2049326	0.87[EUR][1000 genomes]
rs2140432	0.87[EUR][1000 genomes]
rs2177396	0.87[EUR][1000 genomes]
rs2227928	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2227930	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2354860	0.86[EUR][1000 genomes]
rs28617475	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3922730	0.87[EUR][1000 genomes]
rs4273389	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4413348	0.87[EUR][1000 genomes]
rs4597728	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6414350	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440086	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6440087	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6440088	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6440089	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6440090	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440091	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440092	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440093	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440094	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440098	0.86[EUR][1000 genomes]
rs6440099	0.87[EUR][1000 genomes]
rs6770155	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6775583	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6775718	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6775813	0.87[EUR][1000 genomes]
rs6780250	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6782400	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6783203	0.87[EUR][1000 genomes]
rs6784089	0.87[EUR][1000 genomes]
rs6785675	0.87[EUR][1000 genomes]
rs6791816	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6792259	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799752	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6802734	0.82[EUR][1000 genomes]
rs6802774	0.83[EUR][1000 genomes]
rs7428496	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7609842	0.81[EUR][1000 genomes]
rs7610557	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7615316	0.87[EUR][1000 genomes]
rs7623524	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7630130	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7631313	0.86[EUR][1000 genomes]
rs7634158	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7635146	0.86[EUR][1000 genomes]
rs7641330	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646880	0.87[EUR][1000 genomes]
rs7647573	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7651071	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7651542	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9683085	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9808914	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9808943	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9816736	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9820353	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9820770	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9824176	0.81[EUR][1000 genomes]
rs9824893	0.87[EUR][1000 genomes]
rs9825207	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828178	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9846960	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855140	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9855919	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9866958	0.86[EUR][1000 genomes]
rs9869842	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9876254	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9879995	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9882763	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv591919	chr3:142219542-142308070	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:177 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142293800-142298400	Active TSS	GM12878-XiMat	blood
2	chr3:142296000-142298400	Active TSS	K562	blood
3	chr3:142296200-142298200	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr3:142296200-142298200	Active TSS	NHLF	lung
5	chr3:142296200-142298400	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr3:142296200-142298400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:142296200-142298400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:142296200-142298400	Active TSS	Psoas Muscle	Psoas
9	chr3:142296200-142298400	Active TSS	Stomach Smooth Muscle	stomach
10	chr3:142296200-142298600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:142296400-142298200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:142296400-142298200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:142296400-142298200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:142296400-142298200	Active TSS	Left Ventricle	heart
15	chr3:142296400-142298200	Active TSS	A549	lung
16	chr3:142296400-142298400	Active TSS	H1 Cell Line	embryonic stem cell
17	chr3:142296400-142298400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:142296400-142298400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:142296400-142298400	Active TSS	Colonic Mucosa	Colon
20	chr3:142296400-142298400	Active TSS	Fetal Intestine Large	intestine
21	chr3:142296400-142298400	Active TSS	Right Ventricle	heart
22	chr3:142296400-142298400	Active TSS	HSMMtube	muscle
23	chr3:142296400-142298400	Active TSS	NHDF-Ad	bronchial
24	chr3:142296400-142298600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:142296600-142298200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:142296600-142298200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr3:142296600-142298200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:142296600-142298200	Active TSS	Aorta	Aorta
29	chr3:142296600-142298200	Active TSS	Esophagus	oesophagus
30	chr3:142296600-142298200	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr3:142296600-142298200	Active TSS	Ovary	ovary
32	chr3:142296600-142298200	Active TSS	Sigmoid Colon	Sigmoid Colon
33	chr3:142296600-142298400	Active TSS	H9 Cell Line	embryonic stem cell
34	chr3:142296600-142298400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:142296600-142298400	Active TSS	Fetal Muscle Trunk	muscle
36	chr3:142296600-142298600	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr3:142296600-142298600	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr3:142296800-142298200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:142296800-142298200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:142296800-142298200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:142296800-142298200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:142296800-142298200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:142296800-142298200	Active TSS	Fetal Intestine Small	intestine
44	chr3:142296800-142298200	Active TSS	Fetal Kidney	kidney
45	chr3:142296800-142298200	Active TSS	Lung	lung
46	chr3:142296800-142298200	Active TSS	Pancreas	Pancrea
47	chr3:142296800-142298200	Active TSS	Placenta Amnion	Placenta Amnion
48	chr3:142296800-142298200	Active TSS	Dnd41	blood
49	chr3:142296800-142298200	Bivalent/Poised TSS	HepG2	liver
50	chr3:142296800-142298200	Active TSS	NH-A	brain

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