Variant report

Variant	rs41289825
Chromosome Location	chr6:139695632-139695633
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	REST	chr6:139695575-139695938	A549	lung:	n/a	n/a
2	SIN3AK20	chr6:139695226-139696068	K562	blood:	n/a	n/a
3	STAT1	chr6:139695586-139696093	GM12878	blood:	n/a	n/a
4	USF2	chr6:139695597-139696098	H1-hESC	embryonic stem cell:	n/a	chr6:139695925-139695941 chr6:139695919-139695935 chr6:139695683-139695699 chr6:139695931-139695940 chr6:139695931-139695940
5	TAF1	chr6:139695400-139696805	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr6:139695228-139696047	GM12891	blood:	n/a	n/a
7	CUX1	chr6:139695472-139695900	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:139694821-139695993	A549	lung:	n/a	n/a
9	ZNF143	chr6:139694983-139695903	Hela-S3	cervix:	n/a	chr6:139695205-139695223
10	REST	chr6:139695364-139696078	PFSK-1	brain:	n/a	n/a
11	PML	chr6:139695245-139696221	K562	blood:	n/a	n/a
12	POLR2A	chr6:139695339-139695945	GM12891	blood:	n/a	n/a
13	SPI1	chr6:139695069-139696014	HL-60	blood:	n/a	chr6:139695092-139695101
14	POLR2A	chr6:139695302-139696067	GM10847	blood:	n/a	n/a
15	POLR2A	chr6:139694252-139697200	GM18505	blood:	n/a	n/a
16	RFX5	chr6:139695494-139696006	K562	blood:	n/a	n/a
17	MAX	chr6:139695347-139697242	K562	blood:	n/a	chr6:139696216-139696226 chr6:139695931-139695940 chr6:139696718-139696727 chr6:139696040-139696050
18	REST	chr6:139695571-139695883	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr6:139694866-139696167	HUVEC	blood vessel:	n/a	n/a
20	ZBTB7A	chr6:139694492-139696289	K562	blood:	n/a	n/a
21	NANOG	chr6:139695616-139695931	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr6:139695557-139695872	Lung_OC	lung:	n/a	n/a
23	RCOR1	chr6:139694129-139695885	K562	blood:	n/a	n/a
24	EP300	chr6:139695561-139697192	HepG2	liver:	n/a	chr6:139695851-139695860 chr6:139696516-139696532 chr6:139695950-139695966 chr6:139695923-139695939 chr6:139695921-139695930 chr6:139695951-139695967
25	CEBPD	chr6:139695410-139696073	HepG2	liver:	n/a	n/a
26	POLR2A	chr6:139694727-139697278	HepG2	liver:	n/a	n/a
27	CTCF	chr6:139695600-139695750	NHDF-neo	bronchial:	n/a	n/a
28	USF1	chr6:139695363-139695982	SK-N-SH	brain:	n/a	chr6:139695925-139695941 chr6:139695919-139695935 chr6:139695683-139695699 chr6:139695931-139695940 chr6:139695931-139695940
29	CHD2	chr6:139695326-139697298	HepG2	liver:	n/a	chr6:139696457-139696467
30	CTCF	chr6:139695560-139695710	NHEK	skin:	n/a	n/a
31	EP300	chr6:139695271-139696970	ECC-1	luminal epithelium:	n/a	chr6:139695851-139695860 chr6:139696516-139696532 chr6:139695950-139695966 chr6:139695923-139695939 chr6:139695921-139695930 chr6:139695951-139695967
32	TEAD4	chr6:139695467-139695966	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr6:139695396-139696138	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr6:139690635-139697449	SK-N-MC	brain:	n/a	n/a
35	MAX	chr6:139694359-139697524	NB4	blood:	n/a	chr6:139696216-139696226 chr6:139697320-139697330 chr6:139695931-139695940 chr6:139696718-139696727 chr6:139696040-139696050
36	CHD2	chr6:139695225-139696113	H1-hESC	embryonic stem cell:	n/a	n/a
37	POU2F2	chr6:139695419-139696031	GM12891	blood:	n/a	chr6:139695975-139695987 chr6:139695918-139695930
38	RELA	chr6:139695260-139696015	GM18505	blood:	n/a	n/a
39	POLR2A	chr6:139694269-139695957	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr6:139695297-139695954	HepG2	liver:	n/a	n/a
41	RAD21	chr6:139695234-139697389	MCF-7	breast:	n/a	chr6:139696115-139696129 chr6:139696453-139696463
42	ZMIZ1	chr6:139695312-139697003	K562	blood:	n/a	n/a
43	ZNF384	chr6:139695256-139697537	K562	blood:	n/a	n/a
44	REST	chr6:139695327-139696063	A549	lung:	n/a	n/a
45	KAP1	chr6:139695381-139695920	HEK293	kidney:	n/a	n/a
46	USF1	chr6:139695389-139696178	ECC-1	luminal epithelium:	n/a	chr6:139695925-139695941 chr6:139695919-139695935 chr6:139695683-139695699 chr6:139695931-139695940 chr6:139695931-139695940
47	FOS	chr6:139695285-139695924	MCF10A-Er-Src	breast:	n/a	chr6:139695850-139695859
48	POLR2A	chr6:139694315-139697397	MCF-7	breast:	n/a	n/a
49	POU2F2	chr6:139695503-139695969	GM12878	blood:	n/a	chr6:139695918-139695930
50	SMARCB1	chr6:139694375-139697184	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:139695593-139695643	HCPEpiC	choroid plexus:	n/a
2	chr6:139695608-139695658	HIPEpiC	eye:	n/a
3	chr6:139695598-139695648	HRPEpiC	eye:	n/a
4	chr6:139695598-139695648	IMR90	lung:	fetal
5	chr6:139695593-139695643	HEEpiC	esophagus:	n/a
6	chr6:139695598-139695648	NB4	blood:	n/a
7	chr6:139695598-139695648	HCT-116	colon:	n/a
8	chr6:139695608-139695658	RPTEC	kidney:	n/a
9	chr6:139695608-139695658	PFSK-1	brain:	n/a
10	chr6:139695608-139695658	HEK293	kidney:	embryo
11	chr6:139695598-139695648	SAEC	small airway:	n/a
12	chr6:139695598-139695648	Hepatocyte	liver:	n/a
13	chr6:139695593-139695643	PANC-1	pancreas:	n/a
14	chr6:139695608-139695658	BE2_C	brain:	n/a
15	chr6:139695598-139695648	BJ	skin:	n/a
16	chr6:139695593-139695643	HIPEpiC	eye:	n/a
17	chr6:139695608-139695658	PANC-1	pancreas:	n/a
18	chr6:139695593-139695643	SKMC	muscle:	n/a
19	chr6:139695598-139695648	AoSMC	blood vessel:	n/a
20	chr6:139695593-139695643	HCF	heart:	n/a
21	chr6:139695608-139695658	GM19239	blood:	n/a
22	chr6:139695608-139695658	LNCaP	prostate:	n/a
23	chr6:139695608-139695658	NT2-D1	testis:	n/a
24	chr6:139695608-139695658	H1-hESC	embryonic stem cell:	embryo
25	chr6:139695593-139695643	GM12892	blood:	n/a
26	chr6:139695608-139695658	HNPCEpiC	eye:	n/a
27	chr6:139695593-139695643	IMR90	lung:	fetal
28	chr6:139695598-139695648	HRE	kidney:	n/a
29	chr6:139695598-139695648	Caco-2	colon:	n/a
30	chr6:139695593-139695643	HepG2	liver:	n/a
31	chr6:139695598-139695648	NH-A	brain:	n/a
32	chr6:139695598-139695648	AG09309	skin:	n/a
33	chr6:139695608-139695658	Caco-2	colon:	n/a
34	chr6:139695608-139695658	AG04449	skin:	fetal
35	chr6:139695608-139695658	HPAEpiC	pulmonary alveolar:	n/a
36	chr6:139695593-139695643	HMEC	breast:	n/a
37	chr6:139695598-139695648	HepG2	liver:	n/a
38	chr6:139695608-139695658	HRCEpiC	kidney:	n/a
39	chr6:139695598-139695648	AG04450	lung:	fetal
40	chr6:139695598-139695648	HMEC	breast:	n/a
41	chr6:139695608-139695658	GM12878	blood:	n/a
42	chr6:139695598-139695648	SK-N-MC	brain:	n/a
43	chr6:139695608-139695658	SK-N-SH_RA	brain:	n/a
44	chr6:139695593-139695643	HUVEC	blood vessel:	n/a
45	chr6:139695608-139695658	HepG2	liver:	n/a
46	chr6:139695598-139695648	HCF	heart:	n/a
47	chr6:139695598-139695648	HPAEpiC	pulmonary alveolar:	n/a
48	chr6:139695593-139695643	GM12878	blood:	n/a
49	chr6:139695598-139695648	MCF10A-Er-Src	breast:	n/a
50	chr6:139695593-139695643	SK-N-SH	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:131132367..131133184-chr6:139695314..139695954,2	NB4	blood:
2	chr19:47291543..47292245-chr6:139695302..139695945,2	NB4	blood:
3	chr6:139690842..139699833-chr6:139972012..139982796,35	MCF-7	breast:
4	chr6:139307430..139310303-chr6:139693869..139695917,2	K562	blood:
5	chr6:139695534..139696531-chr9:4741015..4741803,2	NB4	blood:
6	chr6:139692335..139698075-chr6:140197375..140205470,17	MCF-7	breast:
7	chr6:33239392..33240337-chr6:139695212..139695901,2	HCT-116	colon:
8	chr19:8372858..8373383-chr6:139695408..139695990,2	NB4	blood:
9	chr6:139691043..139697550-chr6:139974067..139981700,17	MCF-7	breast:
10	chr20:45318318..45318951-chr6:139694885..139695808,2	Hela-S3	cervix:
11	chr6:139348526..139351688-chr6:139694110..139698465,3	MCF-7	breast:
12	chr11:65269344..65269935-chr6:139695402..139696186,2	HCT-116	colon:
13	chr6:139694169..139695837-chr6:140173549..140176425,2	K562	blood:
14	chr12:7053046..7053767-chr6:139695337..139695861,2	NB4	blood:
15	chr17:74099527..74100238-chr6:139695270..139695965,2	HCT-116	colon:
16	chr13:115079690..115080235-chr6:139695273..139696049,2	NB4	blood:
17	chr19:48866567..48867418-chr6:139695427..139696221,2	NB4	blood:
18	chr6:139694055..139695955-chr6:140478931..140481857,2	K562	blood:
19	chr6:139455520..139458326-chr6:139694327..139697443,3	K562	blood:
20	chr6:139692969..139697282-chr6:140197638..140202883,9	MCF-7	breast:
21	chr17:73774534..73776616-chr6:139694816..139697270,2	MCF-7	breast:

Variant related genes	Relation type
CITED2	TF binding region
CITED2	CpG island
ENSG00000223501	Chromatin interaction
ENSG00000252107	Chromatin interaction
ENSG00000231426	Chromatin interaction
ENSG00000182473	Chromatin interaction
ENSG00000111678	Chromatin interaction
ENSG00000105281	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000273217	Chromatin interaction
ENSG00000172315	Chromatin interaction
ENSG00000198824	Chromatin interaction
ENSG00000231500	Chromatin interaction
ENSG00000146386	Chromatin interaction
ENSG00000217128	Chromatin interaction
ENSG00000132475	Chromatin interaction
ENSG00000112406	Chromatin interaction
ENSG00000167775	Chromatin interaction
ENSG00000135597	Chromatin interaction
ENSG00000147853	Chromatin interaction
ENSG00000161558	Chromatin interaction
ENSG00000225148	Chromatin interaction
ENSG00000205695	Chromatin interaction

rs_ID	r²[population]
rs6918767	1.00[ASN][1000 genomes]
rs9495462	1.00[ASN][1000 genomes]
rs9495463	1.00[ASN][1000 genomes]
rs9495464	1.00[ASN][1000 genomes]

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:139690800-139698000	Active TSS	Ovary	ovary
2	chr6:139691000-139697200	Active TSS	Brain Angular Gyrus	brain
3	chr6:139691200-139697600	Active TSS	Fetal Brain Female	brain
4	chr6:139691600-139697600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:139691800-139697600	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr6:139692000-139697600	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr6:139692400-139697600	Active TSS	Brain Cingulate Gyrus	brain
8	chr6:139692800-139697400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:139692800-139697400	Active TSS	Thymus	Thymus
10	chr6:139692800-139697800	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr6:139692800-139697800	Active TSS	Brain Anterior Caudate	brain
12	chr6:139693000-139696000	Active TSS	Primary T cells fromperipheralblood	blood
13	chr6:139693000-139697400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr6:139693000-139697400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:139693200-139697000	Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr6:139693200-139697200	Active TSS	Small Intestine	intestine
17	chr6:139693200-139697400	Active TSS	A549	lung
18	chr6:139693400-139696600	Active TSS	Liver	Liver
19	chr6:139693400-139696800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:139693400-139696800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
21	chr6:139693400-139696800	Active TSS	HMEC	breast
22	chr6:139693400-139697000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:139693400-139697000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:139693400-139697200	Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr6:139693400-139697200	Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr6:139693400-139697400	Active TSS	Primary monocytes fromperipheralblood	blood
27	chr6:139693400-139697400	Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr6:139693400-139697400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:139693400-139697400	Active TSS	Fetal Kidney	kidney
30	chr6:139693400-139697400	Active TSS	GM12878-XiMat	blood
31	chr6:139693400-139697600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:139693400-139697600	Active TSS	Hela-S3	cervix
33	chr6:139693600-139696600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr6:139693600-139696800	Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr6:139693600-139697200	Active TSS	Primary T cells from cord blood	blood
36	chr6:139693600-139697400	Active TSS	H9 Cell Line	embryonic stem cell
37	chr6:139693600-139697400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:139693600-139697400	Active TSS	Monocytes-CD14+_RO01746	blood
39	chr6:139693800-139695800	ZNF genes & repeats	Fetal Brain Male	brain
40	chr6:139693800-139697000	Active TSS	Stomach Mucosa	stomach
41	chr6:139693800-139697400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:139693800-139697400	Active TSS	Brain Substantia Nigra	brain
43	chr6:139694000-139697200	Active TSS	Primary B cells from peripheral blood	blood
44	chr6:139694000-139697200	Bivalent/Poised TSS	HepG2	liver
45	chr6:139694000-139697400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:139694000-139697400	Active TSS	Brain Hippocampus Middle	brain
47	chr6:139694200-139696800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:139694400-139696800	Active TSS	K562	blood
49	chr6:139694400-139697400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:139694400-139697400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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