Variant report

Variant	rs3181230
Chromosome Location	chr6:24659482-24659483
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:91)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:91 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	UBTF	chr6:24659310-24659499	K562	blood:	n/a	n/a
2	TEAD4	chr6:24659023-24659578	K562	blood:	n/a	n/a
3	MAFF	chr6:24659048-24659749	K562	blood:	n/a	n/a
4	TBP	chr6:24659002-24660174	Hela-S3	cervix:	n/a	n/a
5	NFYB	chr6:24659117-24659592	Hela-S3	cervix:	n/a	n/a
6	MAX	chr6:24659242-24659733	H1-hESC	embryonic stem cell:	n/a	n/a
7	CEBPB	chr6:24659020-24659529	K562	blood:	n/a	n/a
8	EP300	chr6:24658834-24660023	A549	lung:	n/a	n/a
9	POLR2A	chr6:24658796-24660257	A549	lung:	n/a	n/a
10	FOS	chr6:24659047-24659985	MCF10A-Er-Src	breast:	n/a	n/a
11	TCF12	chr6:24658810-24659926	A549	lung:	n/a	chr6:24659752-24659761
12	GTF2F1	chr6:24659054-24660238	Hela-S3	cervix:	n/a	n/a
13	MAX	chr6:24659299-24659732	K562	blood:	n/a	n/a
14	RCOR1	chr6:24659045-24659707	K562	blood:	n/a	n/a
15	CHD2	chr6:24659067-24660219	Hela-S3	cervix:	n/a	n/a
16	ATF1	chr6:24659213-24659561	K562	blood:	n/a	n/a
17	SP1	chr6:24658815-24659964	A549	lung:	n/a	n/a
18	MAX	chr6:24659081-24659757	A549	lung:	n/a	n/a
19	POLR2A	chr6:24659477-24659782	GM12891	blood:	n/a	n/a
20	JUN	chr6:24659250-24659564	K562	blood:	n/a	n/a
21	FOSL2	chr6:24658881-24659748	A549	lung:	n/a	n/a
22	MYC	chr6:24659173-24660077	Hela-S3	cervix:	n/a	n/a
23	E2F6	chr6:24659256-24659794	A549	lung:	n/a	n/a
24	JUND	chr6:24659204-24659523	H1-hESC	embryonic stem cell:	n/a	n/a
25	SP1	chr6:24658927-24659832	A549	lung:	n/a	n/a
26	MAFK	chr6:24659120-24659512	IMR90	lung:	n/a	n/a
27	EP300	chr6:24659013-24660585	Hela-S3	cervix:	n/a	n/a
28	CEBPB	chr6:24659122-24659538	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr6:24659050-24659757	Hela-S3	cervix:	n/a	n/a
30	IRF1	chr6:24659204-24659518	K562	blood:	n/a	n/a
31	E2F6	chr6:24659280-24659793	H1-hESC	embryonic stem cell:	n/a	n/a
32	CEBPB	chr6:24659014-24660155	Hela-S3	cervix:	n/a	n/a
33	STAT3	chr6:24658962-24660175	Hela-S3	cervix:	n/a	n/a
34	MAFK	chr6:24659132-24660225	Hela-S3	cervix:	n/a	n/a
35	ZBTB33	chr6:24659079-24659493	A549	lung:	n/a	n/a
36	CEBPB	chr6:24658857-24660171	A549	lung:	n/a	n/a
37	CEBPB	chr6:24659027-24659583	A549	lung:	n/a	n/a
38	POLR2A	chr6:24659043-24659671	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr6:24659082-24660761	Hela-S3	cervix:	n/a	n/a
40	TBL1XR1	chr6:24658515-24659827	K562	blood:	n/a	n/a
41	UBTF	chr6:24659193-24659650	K562	blood:	n/a	n/a
42	MAX	chr6:24659083-24659820	A549	lung:	n/a	n/a
43	POLR2A	chr6:24659036-24660556	Hela-S3	cervix:	n/a	n/a
44	MAX	chr6:24658993-24659943	A549	lung:	n/a	n/a
45	USF2	chr6:24659188-24660156	Hela-S3	cervix:	n/a	chr6:24659604-24659615
46	POLR2A	chr6:24659232-24659650	K562	blood:	n/a	n/a
47	JUND	chr6:24659005-24659558	A549	lung:	n/a	n/a
48	TCF7L2	chr6:24659192-24659564	Hela-S3	cervix:	n/a	n/a
49	CREB1	chr6:24659111-24659590	H1-hESC	embryonic stem cell:	n/a	n/a
50	RCOR1	chr6:24659160-24659582	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:24645670..24648708-chr6:24654981..24659486,5	MCF-7	breast:
2	chr6:24645396..24648552-chr6:24658188..24661192,4	K562	blood:
3	chr6:24645396..24648521-chr6:24658092..24661192,3	K562	blood:
4	chr6:24657655..24659922-chr6:24720349..24722391,2	K562	blood:

No data

Variant related genes	Relation type
TDP2	TF binding region
ENSG00000112308	Chromatin interaction
ENSG00000137261	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs16889592	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs16901739	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17249687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1883591	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2056998	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073013	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2294686	0.91[GIH][hapmap];0.90[MEX][hapmap]
rs2294688	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294689	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2328847	0.86[ASN][1000 genomes]
rs2876679	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3181233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181235	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3181236	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3181237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3212228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3212229	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3212234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212235	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756815	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7765052	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9356944	0.91[GIH][hapmap];0.90[MEX][hapmap]
rs9358786	0.88[ASN][1000 genomes]
rs9358787	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9366579	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9379679	0.92[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9379682	0.98[ASN][1000 genomes]
rs9379686	0.91[GIH][hapmap];0.90[MEX][hapmap]
rs9393575	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9461050	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9467251	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9467253	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9467257	0.81[AMR][1000 genomes];0.95[ASN][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	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv601164	chr6:24625091-24661599	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv601165	chr6:24632642-24666007	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24646800-24662400	Weak transcription	Right Ventricle	heart
2	chr6:24646800-24662600	Weak transcription	Spleen	Spleen
3	chr6:24646800-24666000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:24647000-24662200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:24647000-24662400	Weak transcription	Lung	lung
6	chr6:24647000-24662600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:24647000-24666400	Weak transcription	Esophagus	oesophagus
8	chr6:24647200-24663400	Weak transcription	Fetal Kidney	kidney
9	chr6:24649400-24659600	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr6:24649400-24664800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:24649400-24665200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:24650000-24663600	Strong transcription	Dnd41	blood
13	chr6:24650000-24665000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:24651000-24659800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr6:24652400-24662800	Weak transcription	Psoas Muscle	Psoas
16	chr6:24653400-24662600	Weak transcription	NHLF	lung
17	chr6:24653600-24660000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr6:24653800-24662200	Weak transcription	Fetal Stomach	stomach
19	chr6:24653800-24662200	Weak transcription	Ovary	ovary
20	chr6:24653800-24662400	Weak transcription	Colonic Mucosa	Colon
21	chr6:24653800-24662600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:24653800-24663800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:24653800-24666200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:24654000-24662600	Weak transcription	HSMMtube	muscle
25	chr6:24654000-24663200	Weak transcription	Fetal Brain Male	brain
26	chr6:24654000-24665200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr6:24654200-24661600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:24654200-24661600	Weak transcription	Brain Hippocampus Middle	brain
29	chr6:24654200-24662200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr6:24654200-24662400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:24654200-24662400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr6:24654200-24663400	Weak transcription	Brain Anterior Caudate	brain
33	chr6:24654200-24664400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr6:24654200-24665000	Weak transcription	Brain Substantia Nigra	brain
35	chr6:24654200-24665000	Weak transcription	Fetal Lung	lung
36	chr6:24654400-24662200	Weak transcription	Fetal Brain Female	brain
37	chr6:24654400-24662400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr6:24654400-24663200	Weak transcription	Brain Angular Gyrus	brain
39	chr6:24654400-24665200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr6:24655000-24662600	Weak transcription	Liver	Liver
41	chr6:24655400-24665000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:24656000-24662600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr6:24656000-24662800	Weak transcription	Pancreas	Pancrea
44	chr6:24656000-24663000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr6:24656000-24663600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr6:24656000-24663800	Strong transcription	Fetal Thymus	thymus
47	chr6:24656200-24662200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:24656200-24662200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:24656200-24662400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr6:24656200-24662400	Weak transcription	Left Ventricle	heart

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