Variant report

Variant	rs4750075
Chromosome Location	chr10:6246469-6246470
allele	C/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	REST	chr10:6246114-6247425	A549	lung:	n/a	n/a
2	MXI1	chr10:6242644-6247076	SK-N-SH	brain:	n/a	n/a
3	TAF1	chr10:6245810-6247232	A549	lung:	n/a	n/a
4	TCF12	chr10:6243574-6247500	A549	lung:	n/a	chr10:6244120-6244127 chr10:6244121-6244131
5	POLR2A	chr10:6245863-6246753	A549	lung:	n/a	n/a
6	USF1	chr10:6246356-6247263	A549	lung:	n/a	n/a
7	POLR2A	chr10:6246239-6247300	GM12891	blood:	n/a	n/a
8	E2F6	chr10:6245470-6246543	H1-hESC	embryonic stem cell:	n/a	chr10:6245722-6245734 chr10:6245926-6245936
9	SP1	chr10:6244436-6247427	A549	lung:	n/a	chr10:6246476-6246486
10	POU2F2	chr10:6246013-6247234	GM12878	blood:	n/a	chr10:6246755-6246763 chr10:6246817-6246828 chr10:6246750-6246768 chr10:6246818-6246828 chr10:6246749-6246770 chr10:6246814-6246832
11	MAX	chr10:6244130-6246578	MCF-7	breast:	n/a	chr10:6244170-6244180 chr10:6244173-6244183
12	POLR2A	chr10:6245827-6247121	H1-hESC	embryonic stem cell:	n/a	n/a
13	MYC	chr10:6245868-6246699	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr10:6246291-6246592	MCF10A-Er-Src	breast:	n/a	n/a
15	SMC3	chr10:6242512-6247173	SK-N-SH	brain:	n/a	chr10:6245922-6245932 chr10:6243015-6243025
16	POLR2A	chr10:6244438-6246716	MCF10A-Er-Src	breast:	n/a	n/a
17	JUND	chr10:6246200-6247243	A549	lung:	n/a	n/a
18	MAX	chr10:6246122-6246627	SK-N-SH	brain:	n/a	n/a
19	MYC	chr10:6246387-6246780	MCF10A-Er-Src	breast:	n/a	n/a
20	BCL3	chr10:6246338-6247184	A549	lung:	n/a	n/a
21	CTCF	chr10:6243513-6247466	A549	lung:	n/a	chr10:6244171-6244184 chr10:6246034-6246047 chr10:6245938-6245951 chr10:6246241-6246254 chr10:6245941-6245954
22	FOSL2	chr10:6246323-6247494	A549	lung:	n/a	n/a
23	POLR2A	chr10:6246049-6247266	GM12891	blood:	n/a	n/a
24	POLR2A	chr10:6244581-6247062	K562	blood:	n/a	n/a
25	CREB1	chr10:6246011-6246605	A549	lung:	n/a	n/a
26	HA-E2F1	chr10:6244414-6246646	MCF-7	breast:	n/a	chr10:6245722-6245734 chr10:6245926-6245936
27	EBF1	chr10:6245966-6246971	GM12878	blood:	n/a	chr10:6246715-6246724 chr10:6246715-6246724 chr10:6246713-6246726 chr10:6246713-6246724
28	POLR2A	chr10:6245839-6246687	A549	lung:	n/a	n/a
29	YY1	chr10:6246451-6246734	A549	lung:	n/a	n/a
30	BCL3	chr10:6246342-6247374	A549	lung:	n/a	n/a
31	POLR2A	chr10:6246010-6247458	U87	brain:	n/a	n/a
32	FOS	chr10:6246310-6246654	MCF10A-Er-Src	breast:	n/a	n/a
33	MAX	chr10:6245923-6246584	ECC-1	luminal epithelium:	n/a	n/a
34	GATA3	chr10:6244277-6247528	A549	lung:	n/a	n/a
35	POLR2A	chr10:6246277-6247373	U87	brain:	n/a	n/a
36	FOXA2	chr10:6246325-6247077	A549	lung:	n/a	n/a
37	MAX	chr10:6242769-6246556	A549	lung:	n/a	chr10:6244170-6244180 chr10:6243866-6243875 chr10:6244173-6244183
38	JUND	chr10:6245865-6246722	A549	lung:	n/a	n/a
39	MAX	chr10:6245778-6246557	MCF-7	breast:	n/a	n/a
40	MXI1	chr10:6244137-6247434	IMR90	lung:	n/a	n/a
41	POLR2A	chr10:6245859-6246666	A549	lung:	n/a	n/a
42	SIN3A	chr10:6243532-6247000	H1-hESC	embryonic stem cell:	n/a	chr10:6244188-6244202 chr10:6246143-6246154
43	POLR2A	chr10:6246010-6247464	U87	brain:	n/a	n/a
44	ESRRA	chr10:6244303-6246654	GM12878	blood:	n/a	n/a
45	NFIC	chr10:6246167-6246734	SK-N-SH	brain:	n/a	n/a
46	E2F4	chr10:6246388-6246684	MCF10A-Er-Src	breast:	n/a	n/a
47	FOSL2	chr10:6246181-6246737	SK-N-SH	brain:	n/a	n/a
48	FOS	chr10:6246258-6246761	MCF10A-Er-Src	breast:	n/a	n/a
49	RAD21	chr10:6246272-6246798	IMR90	lung:	n/a	n/a
50	POLR2A	chr10:6242449-6247290	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:6129825..6133257-chr10:6241985..6247329,10	MCF-7	breast:
2	chr10:6183735..6189299-chr10:6241759..6246920,10	MCF-7	breast:
3	chr10:6245082..6247661-chr9:91147129..91149982,2	MCF-7	breast:
4	chr10:6143166..6145739-chr10:6245064..6246579,2	K562	blood:
5	chr10:6243696..6246547-chr17:56707857..56709473,2	MCF-7	breast:
6	chr10:6244869..6246858-chr17:56708954..56710918,2	MCF-7	breast:
7	chr10:6192153..6194563-chr10:6245038..6246551,2	MCF-7	breast:
8	chr10:6183938..6190482-chr10:6242008..6247032,17	MCF-7	breast:
9	chr10:6243668..6247308-chr10:6319585..6323356,5	MCF-7	breast:
10	chr10:6245084..6247522-chr10:6358973..6361369,2	MCF-7	breast:
11	chr10:6198072..6199793-chr10:6244896..6246657,2	MCF-7	breast:
12	chr10:6242187..6248014-chr10:6262246..6271624,18	MCF-7	breast:
13	chr10:6132741..6135647-chr10:6244936..6248119,3	MCF-7	breast:
14	chr10:6128377..6132115-chr10:6241834..6247197,6	MCF-7	breast:
15	chr10:6149112..6154904-chr10:6241492..6247373,13	MCF-7	breast:
16	chr10:6189894..6192661-chr10:6244759..6246996,2	MCF-7	breast:
17	chr10:6244071..6246577-chr11:62606915..62609638,2	MCF-7	breast:
18	chr10:6145584..6148508-chr10:6244741..6246500,2	MCF-7	breast:
19	chr10:6245444..6247830-chr10:6297779..6300544,2	MCF-7	breast:
20	chr10:6244951..6247440-chr10:6279322..6281493,5	MCF-7	breast:
21	chr10:6245319..6247600-chr17:59477846..59479369,2	MCF-7	breast:
22	chr10:6240729..6242580-chr10:6245113..6247243,2	K562	blood:
23	chr10:5930925..5933506-chr10:6244058..6246915,2	MCF-7	breast:
24	chr10:6242739..6248482-chr10:6257769..6263853,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213994	TF binding region
ENSG00000215244	Chromatin interaction
ENSG00000134461	Chromatin interaction
ENSG00000263628	Chromatin interaction
ENSG00000201581	Chromatin interaction
ENSG00000134453	Chromatin interaction
ENSG00000134452	Chromatin interaction
ENSG00000170525	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000133316	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11257259	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794983	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4747921	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57770060	0.90[ASN][1000 genomes]
rs61297532	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72777862	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1040721	chr10:6155144-6322566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv540476	chr10:6155144-6322566	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv894817	chr10:6173416-6251252	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
6	nsv1041039	chr10:6217724-6354858	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv894832	chr10:6237156-6253651	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv894833	chr10:6237156-6261704	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv894834	chr10:6237156-6272169	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	nsv521145	chr10:6241803-6246678	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv894835	chr10:6242176-6268422	Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 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	chr10:6242800-6246600	Active TSS	Placenta Amnion	Placenta Amnion
2	chr10:6242800-6246600	Active TSS	Psoas Muscle	Psoas
3	chr10:6242800-6247000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr10:6242800-6247400	Active TSS	Fetal Kidney	kidney
5	chr10:6242800-6247800	Active TSS	Aorta	Aorta
6	chr10:6243000-6246600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr10:6243600-6246600	Active TSS	HSMMtube	muscle
8	chr10:6243600-6247200	Flanking Active TSS	Liver	Liver
9	chr10:6243600-6247200	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr10:6243800-6247400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
11	chr10:6244200-6246800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr10:6244400-6246600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr10:6244400-6246600	Active TSS	Small Intestine	intestine
14	chr10:6244600-6246600	Active TSS	H9 Cell Line	embryonic stem cell
15	chr10:6244600-6246600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr10:6244600-6246600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr10:6244600-6246600	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr10:6244600-6246600	Active TSS	HSMM	muscle
19	chr10:6244600-6246600	Active TSS	NH-A	brain
20	chr10:6244600-6246600	Active TSS	NHLF	lung
21	chr10:6244600-6246800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr10:6244600-6246800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr10:6244600-6246800	Active TSS	Brain Anterior Caudate	brain
24	chr10:6244600-6246800	Active TSS	Gastric	stomach
25	chr10:6244600-6247200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr10:6244600-6247600	Active TSS	Esophagus	oesophagus
27	chr10:6244600-6249400	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr10:6244800-6246600	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr10:6244800-6246800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr10:6245000-6246600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr10:6245000-6246600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr10:6245600-6246800	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr10:6245600-6247000	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr10:6245600-6247000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr10:6245600-6247400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr10:6245600-6247400	Transcr. at gene 5' and 3'	A549	lung
37	chr10:6245600-6247400	Transcr. at gene 5' and 3'	Dnd41	blood
38	chr10:6245800-6246600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
39	chr10:6245800-6246600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
40	chr10:6245800-6246600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
41	chr10:6245800-6246800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr10:6245800-6246800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
43	chr10:6245800-6246800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr10:6245800-6246800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
45	chr10:6245800-6247000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr10:6245800-6247000	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
47	chr10:6245800-6247200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr10:6245800-6247200	Flanking Active TSS	Pancreas	Pancrea
49	chr10:6246000-6246600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr10:6246000-6246600	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon

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