Variant report

Variant	rs61845943
Chromosome Location	chr10:28592192-28592193
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	POLR2A	chr10:28591323-28592495	H1-neurons	neurons:	n/a	n/a
2	ELF1	chr10:28591580-28592429	GM12878	blood:	n/a	chr10:28591906-28591918 chr10:28591922-28591934 chr10:28591958-28591970
3	JUND	chr10:28592182-28592518	H1-hESC	embryonic stem cell:	n/a	chr10:28592415-28592424
4	RAD21	chr10:28592140-28592351	HepG2	liver:	n/a	n/a
5	GATA1	chr10:28591895-28592654	PBDE	blood:	n/a	n/a
6	MYC	chr10:28591706-28592425	K562	blood:	n/a	chr10:28591998-28592008 chr10:28591963-28591973
7	CTCF	chr10:28592160-28592310	Caco-2	colon:	n/a	n/a
8	CREB1	chr10:28591581-28592389	A549	lung:	n/a	n/a
9	TAF1	chr10:28592083-28592447	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr10:28592051-28592430	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr10:28591384-28592488	MCF-7	breast:	n/a	chr10:28591998-28592008 chr10:28591963-28591973
12	RAD21	chr10:28591438-28592471	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr10:28591619-28592404	HepG2	liver:	n/a	n/a
14	MYBL2	chr10:28592132-28592594	HepG2	liver:	n/a	n/a
15	FOS	chr10:28591933-28592325	K562	blood:	n/a	chr10:28592035-28592044 chr10:28592169-28592178
16	ATF1	chr10:28591972-28592304	K562	blood:	n/a	n/a
17	UBTF	chr10:28591329-28592283	K562	blood:	n/a	n/a
18	POLR2A	chr10:28591493-28592488	MCF-7	breast:	n/a	n/a
19	YY1	chr10:28591528-28592395	HepG2	liver:	n/a	chr10:28591795-28591806 chr10:28591700-28591714 chr10:28591963-28591977
20	MXI1	chr10:28591818-28592344	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr10:28591499-28592590	ProgFib	skin:	n/a	n/a
22	MYC	chr10:28592185-28592367	MCF-7	breast:	n/a	n/a
23	RUNX3	chr10:28591635-28592387	GM12878	blood:	n/a	chr10:28592202-28592219
24	MAX	chr10:28591586-28592406	K562	blood:	n/a	chr10:28591998-28592008 chr10:28591963-28591973
25	RFX5	chr10:28591587-28592811	SK-N-SH	brain:	n/a	n/a
26	CTCF	chr10:28592147-28592365	Lung_OC	lung:	n/a	n/a
27	CREB1	chr10:28591887-28592328	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr10:28591533-28592348	K562	blood:	n/a	chr10:28591813-28591826 chr10:28591834-28591847 chr10:28591656-28591669
29	POLR2A	chr10:28592048-28592425	ECC-1	luminal epithelium:	n/a	n/a
30	RCOR1	chr10:28591769-28592370	Hela-S3	cervix:	n/a	n/a
31	ZNF143	chr10:28591685-28592345	H1-hESC	embryonic stem cell:	n/a	chr10:28591700-28591710 chr10:28591960-28591970 chr10:28592048-28592058
32	EP300	chr10:28592112-28592335	GM12878	blood:	n/a	n/a
33	SP1	chr10:28591774-28592356	K562	blood:	n/a	chr10:28591965-28591974 chr10:28592031-28592041 chr10:28592012-28592021 chr10:28592032-28592046 chr10:28592037-28592046 chr10:28592030-28592042 chr10:28592030-28592042 chr10:28591964-28591978 chr10:28592036-28592045 chr10:28592160-28592181 chr10:28592031-28592041 chr10:28592010-28592022 chr10:28591963-28591975 chr10:28592031-28592040 chr10:28592010-28592022 chr10:28592032-28592041 chr10:28592030-28592041 chr10:28592035-28592047 chr10:28592035-28592047 chr10:28592032-28592041 chr10:28592037-28592046
34	MXI1	chr10:28591239-28592576	IMR90	lung:	n/a	n/a
35	CTCF	chr10:28592180-28592330	HPF	lung:	n/a	n/a
36	TAF1	chr10:28591588-28592477	H1-hESC	embryonic stem cell:	n/a	n/a
37	RFX5	chr10:28591684-28592419	Hela-S3	cervix:	n/a	n/a
38	ZNF143	chr10:28591865-28592444	K562	blood:	n/a	chr10:28591960-28591970 chr10:28592048-28592058
39	FOS	chr10:28592130-28592201	MCF10A-Er-Src	breast:	n/a	chr10:28592169-28592178
40	WRNIP1	chr10:28592051-28592409	GM12878	blood:	n/a	n/a
41	E2F6	chr10:28592145-28592312	K562	blood:	n/a	n/a
42	HEY1	chr10:28591644-28592485	HepG2	liver:	n/a	chr10:28591958-28591973 chr10:28591917-28591932 chr10:28591920-28591935 chr10:28591682-28591697
43	REST	chr10:28592099-28592396	HepG2	liver:	n/a	n/a
44	CHD2	chr10:28591776-28592349	H1-hESC	embryonic stem cell:	n/a	chr10:28592032-28592042
45	RUNX3	chr10:28591712-28592337	GM12878	blood:	n/a	chr10:28592202-28592219
46	MYC	chr10:28591830-28592428	MCF10A-Er-Src	breast:	n/a	chr10:28591998-28592008 chr10:28591963-28591973
47	MYC	chr10:28592129-28592283	MCF10A-Er-Src	breast:	n/a	n/a
48	CBX3	chr10:28591954-28592343	K562	blood:	n/a	n/a
49	POLR2A	chr10:28592104-28592512	HepG2	liver:	n/a	n/a
50	HCFC1	chr10:28591250-28592582	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:28592071..28593938-chr10:28656842..28659307,2	MCF-7	breast:
2	chr10:28570371..28575406-chr10:28590076..28593528,7	MCF-7	breast:
3	chr10:28591768..28592588-chr11:102962835..102963365,2	HCT-116	colon:
4	chr10:28590710..28592646-chr10:28598868..28601462,3	MCF-7	breast:

Variant related genes	Relation type
MPP7	TF binding region
ENSG00000137692	Chromatin interaction
ENSG00000150054	Chromatin interaction
ENSG00000222374	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11006932	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11006955	0.86[AMR][1000 genomes]
rs11006996	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11007002	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12356457	0.89[AFR][1000 genomes]
rs12357385	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61845938	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61845939	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61845945	1.00[ASN][1000 genomes]
rs7090006	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1041555	chr10:28419399-29304934	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv1037863	chr10:28419399-29378871	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv540521	chr10:28419399-29378871	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28589800-28592800	Active TSS	Stomach Smooth Muscle	stomach
2	chr10:28590400-28592800	Active TSS	Aorta	Aorta
3	chr10:28590600-28592600	Active TSS	Brain Anterior Caudate	brain
4	chr10:28590600-28592600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr10:28590600-28592600	Active TSS	Colonic Mucosa	Colon
6	chr10:28590800-28592400	Active TSS	Brain Angular Gyrus	brain
7	chr10:28590800-28592600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr10:28590800-28592600	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr10:28590800-28592600	Active TSS	Brain Germinal Matrix	brain
10	chr10:28590800-28592600	Active TSS	Right Ventricle	heart
11	chr10:28590800-28592800	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr10:28590800-28592800	Active TSS	Fetal Stomach	stomach
13	chr10:28590800-28592800	Active TSS	Right Atrium	heart
14	chr10:28590800-28593000	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr10:28590800-28593200	Active TSS	H1 Cell Line	embryonic stem cell
16	chr10:28591000-28592200	Active TSS	HepG2	liver
17	chr10:28591000-28592400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr10:28591000-28592400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr10:28591000-28592400	Active TSS	Brain Hippocampus Middle	brain
20	chr10:28591000-28592400	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr10:28591000-28592400	Active TSS	Gastric	stomach
22	chr10:28591000-28592400	Active TSS	Rectal Mucosa Donor 31	rectum
23	chr10:28591000-28592600	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr10:28591000-28592600	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr10:28591000-28592600	Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr10:28591000-28592600	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr10:28591000-28592600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr10:28591000-28592600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr10:28591000-28592600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr10:28591000-28592600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr10:28591000-28592600	Active TSS	Brain Cingulate Gyrus	brain
32	chr10:28591000-28592600	Active TSS	Esophagus	oesophagus
33	chr10:28591000-28592600	Active TSS	Fetal Muscle Trunk	muscle
34	chr10:28591000-28592600	Active TSS	Left Ventricle	heart
35	chr10:28591000-28592600	Active TSS	Ovary	ovary
36	chr10:28591000-28592600	Active TSS	Placenta Amnion	Placenta Amnion
37	chr10:28591000-28592800	Active TSS	H9 Cell Line	embryonic stem cell
38	chr10:28591000-28592800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr10:28591000-28592800	Active TSS	Fetal Intestine Large	intestine
40	chr10:28591000-28592800	Active TSS	Fetal Intestine Small	intestine
41	chr10:28591000-28592800	Active TSS	Pancreas	Pancrea
42	chr10:28591000-28592800	Active TSS	Psoas Muscle	Psoas
43	chr10:28591000-28593000	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr10:28591000-28593000	Active TSS	Rectal Smooth Muscle	rectum
45	chr10:28591200-28592200	Active TSS	Primary hematopoietic stem cells	blood
46	chr10:28591200-28592200	Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr10:28591200-28592200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr10:28591200-28592200	Active TSS	NHEK	skin
49	chr10:28591200-28592400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr10:28591200-28592400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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