Variant report

Variant	rs3846060
Chromosome Location	chr3:42696254-42696255
allele	A/C
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	MXI1	chr3:42695902-42696722	HepG2	liver:	n/a	chr3:42696527-42696536 chr3:42696527-42696536 chr3:42696529-42696538
2	POLR2A	chr3:42695783-42696762	HUVEC	blood vessel:	n/a	n/a
3	ELF1	chr3:42695344-42696508	K562	blood:	n/a	chr3:42695919-42695931 chr3:42696029-42696038 chr3:42695623-42695636
4	POLR2A	chr3:42695414-42696432	GM19099	blood:	n/a	n/a
5	TBP	chr3:42696162-42696563	H1-hESC	embryonic stem cell:	n/a	n/a
6	HCFC1	chr3:42695852-42696545	K562	blood:	n/a	n/a
7	ZBTB7A	chr3:42694819-42697395	ECC-1	luminal epithelium:	n/a	chr3:42697295-42697303
8	TEAD4	chr3:42696156-42696583	K562	blood:	n/a	n/a
9	SP1	chr3:42696118-42696604	H1-hESC	embryonic stem cell:	n/a	chr3:42696294-42696303 chr3:42696292-42696304 chr3:42696295-42696308 chr3:42696292-42696304 chr3:42696582-42696592 chr3:42696368-42696379
10	CTCF	chr3:42696180-42696330	GM12872	blood:	n/a	chr3:42696311-42696329 chr3:42696313-42696326
11	POLR2A	chr3:42695499-42696703	HUVEC	blood vessel:	n/a	n/a
12	CTCF	chr3:42696220-42696370	Hela-S3	cervix:	n/a	chr3:42696311-42696329 chr3:42696313-42696326
13	RCOR1	chr3:42696190-42696532	K562	blood:	n/a	n/a
14	E2F1	chr3:42695601-42696694	Hela-S3	cervix:	n/a	chr3:42696396-42696406 chr3:42696132-42696142 chr3:42696399-42696408
15	POLR2A	chr3:42695723-42696282	GM12878	blood:	n/a	n/a
16	GTF2F1	chr3:42696228-42696283	K562	blood:	n/a	n/a
17	HA-E2F1	chr3:42695734-42696880	Hela-S3	cervix:	n/a	chr3:42696396-42696406 chr3:42696132-42696142 chr3:42696399-42696408
18	CTCF	chr3:42696240-42696390	GM12864	blood:	n/a	chr3:42696311-42696329 chr3:42696313-42696326
19	CTCF	chr3:42696220-42696591	H1-hESC	embryonic stem cell:	n/a	chr3:42696311-42696329 chr3:42696313-42696326
20	MAX	chr3:42696020-42696804	H1-hESC	embryonic stem cell:	n/a	chr3:42696527-42696537 chr3:42696528-42696537 chr3:42696528-42696537 chr3:42696530-42696539 chr3:42696528-42696537 chr3:42696527-42696538 chr3:42696527-42696538 chr3:42696528-42696538
21	MAZ	chr3:42695954-42697067	HepG2	liver:	n/a	chr3:42696527-42696537 chr3:42696528-42696537 chr3:42696528-42696537 chr3:42696530-42696539 chr3:42696528-42696537 chr3:42696527-42696538 chr3:42696527-42696538 chr3:42696528-42696538
22	TEAD4	chr3:42696135-42696744	SK-N-SH	brain:	n/a	n/a
23	EP300	chr3:42696128-42696643	H1-hESC	embryonic stem cell:	n/a	chr3:42696395-42696404 chr3:42696346-42696362 chr3:42696465-42696474
24	POLR2A	chr3:42695420-42696776	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr3:42695910-42697257	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAX	chr3:42695481-42696851	SK-N-SH	brain:	n/a	chr3:42696527-42696537 chr3:42696528-42696537 chr3:42696528-42696537 chr3:42696530-42696539 chr3:42696528-42696537 chr3:42696527-42696538 chr3:42696527-42696538 chr3:42696528-42696538
27	POLR2A	chr3:42695428-42696813	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr3:42696120-42696270	HMEC	breast:	n/a	chr3:42696129-42696142
29	TAF1	chr3:42696196-42696609	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr3:42696090-42696881	H1-hESC	embryonic stem cell:	n/a	chr3:42696527-42696537 chr3:42696528-42696537 chr3:42696528-42696537 chr3:42696530-42696539 chr3:42696528-42696537 chr3:42696527-42696538 chr3:42696527-42696538 chr3:42696528-42696538
31	POLR2A	chr3:42696080-42696799	SK-N-MC	brain:	n/a	n/a
32	POLR2A	chr3:42695857-42696429	H1-neurons	neurons:	n/a	n/a
33	POLR2A	chr3:42696085-42696666	U87	brain:	n/a	n/a
34	ZBTB7A	chr3:42695765-42696671	ECC-1	luminal epithelium:	n/a	n/a
35	CTCF	chr3:42695856-42696610	K562	blood:	n/a	chr3:42696129-42696142 chr3:42696311-42696329 chr3:42696313-42696326
36	RAD21	chr3:42696200-42696601	H1-hESC	embryonic stem cell:	n/a	chr3:42696309-42696328 chr3:42696313-42696327
37	MYC	chr3:42695808-42696902	A549	lung:	n/a	chr3:42696527-42696537 chr3:42696528-42696537 chr3:42696528-42696537 chr3:42696530-42696539 chr3:42696528-42696537 chr3:42696527-42696538 chr3:42696527-42696538 chr3:42696528-42696538
38	BACH1	chr3:42695553-42696606	H1-hESC	embryonic stem cell:	n/a	n/a
39	TAF7	chr3:42696142-42696641	H1-hESC	embryonic stem cell:	n/a	n/a
40	ZNF143	chr3:42696054-42696783	H1-hESC	embryonic stem cell:	n/a	chr3:42696528-42696546 chr3:42696453-42696463 chr3:42696395-42696405
41	RAD21	chr3:42696079-42696654	H1-hESC	embryonic stem cell:	n/a	chr3:42696309-42696328 chr3:42696313-42696327 chr3:42696129-42696142
42	SIN3A	chr3:42695461-42696925	H1-hESC	embryonic stem cell:	n/a	chr3:42696529-42696538 chr3:42696132-42696145 chr3:42696458-42696471 chr3:42696527-42696536
43	EGR1	chr3:42695939-42696279	GM12878	blood:	n/a	chr3:42696079-42696093
44	ETS1	chr3:42696144-42696385	K562	blood:	n/a	chr3:42696294-42696305
45	POLR2A	chr3:42694102-42696721	HUVEC	blood vessel:	n/a	n/a
46	E2F6	chr3:42695742-42696779	K562	blood:	n/a	chr3:42696507-42696518 chr3:42696396-42696406 chr3:42696132-42696142 chr3:42696399-42696408
47	CTCF	chr3:42696240-42696390	GM12878	blood:	n/a	chr3:42696311-42696329 chr3:42696313-42696326
48	TEAD4	chr3:42696130-42696634	HepG2	liver:	n/a	n/a
49	TCF12	chr3:42694130-42697494	ECC-1	luminal epithelium:	n/a	chr3:42694507-42694514 chr3:42697092-42697099 chr3:42694856-42694865
50	POLR2A	chr3:42695810-42696624	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:42632553..42639930-chr3:42692933..42696882,8	K562	blood:
2	chr3:42659807..42662376-chr3:42694804..42697042,2	MCF-7	breast:
3	chr3:42695894..42698650-chr3:42786338..42788734,2	K562	blood:
4	chr3:42620456..42625490-chr3:42691753..42697487,7	K562	blood:
5	chr3:42623862..42624421-chr3:42696058..42696857,2	K562	blood:
6	chr3:42629929..42632831-chr3:42695818..42698742,2	MCF-7	breast:
7	chr3:42631026..42632613-chr3:42695067..42697159,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230084	TF binding region
ZBTB47	TF binding region
ENSG00000114857	Chromatin interaction
ENSG00000093183	Chromatin interaction
ENSG00000008324	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs17237090	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56300632	0.86[ASN][1000 genomes]
rs73085333	0.84[ASN][1000 genomes]
rs9833459	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv1818302	chr3:42688867-42709062	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv876731	chr3:42690285-42711655	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 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	chr3:42694000-42696800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:42694400-42697000	Active TSS	Aorta	Aorta
3	chr3:42694600-42696800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:42694800-42696600	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr3:42694800-42696600	Active TSS	Brain Substantia Nigra	brain
6	chr3:42695000-42696400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:42695000-42696400	Active TSS	Small Intestine	intestine
8	chr3:42695000-42696600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:42695000-42696600	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr3:42695000-42696800	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr3:42695000-42696800	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr3:42695000-42696800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:42695000-42696800	Active TSS	Brain Cingulate Gyrus	brain
14	chr3:42695000-42696800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr3:42695200-42696400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:42695200-42696400	Active TSS	HepG2	liver
17	chr3:42695200-42696600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:42695200-42696600	Active TSS	Brain Hippocampus Middle	brain
19	chr3:42695200-42696600	Active TSS	Colon Smooth Muscle	Colon
20	chr3:42695200-42696600	Active TSS	Left Ventricle	heart
21	chr3:42695200-42696600	Active TSS	Ovary	ovary
22	chr3:42695200-42696600	Active TSS	NHLF	lung
23	chr3:42695200-42696800	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr3:42695200-42696800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:42695200-42696800	Active TSS	Brain Angular Gyrus	brain
26	chr3:42695200-42696800	Active TSS	Brain Anterior Caudate	brain
27	chr3:42695200-42696800	Active TSS	Fetal Kidney	kidney
28	chr3:42695200-42696800	Active TSS	Gastric	stomach
29	chr3:42695200-42696800	Active TSS	Right Atrium	heart
30	chr3:42695200-42696800	Active TSS	NHDF-Ad	bronchial
31	chr3:42695400-42696400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:42695400-42696400	Active TSS	Liver	Liver
33	chr3:42695400-42696400	Active TSS	Hela-S3	cervix
34	chr3:42695400-42696400	Active TSS	HSMMtube	muscle
35	chr3:42695400-42696400	Active TSS	Osteobl	bone
36	chr3:42695400-42696600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:42695400-42696600	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr3:42695400-42696600	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr3:42695400-42696600	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr3:42695400-42696600	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr3:42695400-42696600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:42695400-42696600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:42695400-42696600	Active TSS	Lung	lung
44	chr3:42695400-42696600	Active TSS	Psoas Muscle	Psoas
45	chr3:42695400-42696600	Active TSS	Rectal Smooth Muscle	rectum
46	chr3:42695400-42696600	Active TSS	Right Ventricle	heart
47	chr3:42695400-42696600	Active TSS	A549	lung
48	chr3:42695400-42696600	Active TSS	HSMM	muscle
49	chr3:42695400-42696600	Active TSS	NHEK	skin
50	chr3:42695400-42696800	Active TSS	H9 Cell Line	embryonic stem cell

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