Variant report

Variant	rs61838252
Chromosome Location	chr1:223537933-223537934
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	HA-E2F1	chr1:223537180-223538300	MCF-7	breast:	n/a	chr1:223538169-223538176 chr1:223537564-223537574 chr1:223538169-223538176 chr1:223537543-223537552 chr1:223538169-223538176
2	POLR2A	chr1:223537821-223538025	MCF-7	breast:	n/a	n/a
3	POLR2A	chr1:223537872-223538003	MCF-7	breast:	n/a	n/a
4	E2F6	chr1:223537699-223538417	H1-hESC	embryonic stem cell:	n/a	chr1:223538169-223538176 chr1:223538169-223538176 chr1:223538169-223538176 chr1:223538386-223538395 chr1:223538386-223538398 chr1:223538394-223538403
5	MAX	chr1:223537700-223538052	K562	blood:	n/a	n/a
6	E2F6	chr1:223537658-223538020	A549	lung:	n/a	n/a
7	MAX	chr1:223537645-223538736	H1-hESC	embryonic stem cell:	n/a	n/a
8	E2F6	chr1:223537730-223538027	A549	lung:	n/a	n/a
9	MAX	chr1:223537289-223538072	MCF-7	breast:	n/a	chr1:223537542-223537552
10	NFYB	chr1:223537729-223538016	K562	blood:	n/a	chr1:223537834-223537848 chr1:223537834-223537849 chr1:223537834-223537849
11	USF1	chr1:223537681-223537991	H1-hESC	embryonic stem cell:	n/a	chr1:223537859-223537875
12	NFYB	chr1:223537713-223538047	GM12878	blood:	n/a	chr1:223537834-223537848 chr1:223537834-223537849 chr1:223537834-223537849
13	E2F6	chr1:223537700-223538243	K562	blood:	n/a	chr1:223538169-223538176 chr1:223538169-223538176 chr1:223538169-223538176
14	MAX	chr1:223537252-223538363	H1-hESC	embryonic stem cell:	n/a	chr1:223537542-223537552
15	E2F6	chr1:223537688-223537961	K562	blood:	n/a	n/a
16	MAX	chr1:223537702-223537969	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr1:223537784-223538001	MCF-7	breast:	n/a	n/a
18	MAX	chr1:223537676-223538019	A549	lung:	n/a	n/a
19	CTBP2	chr1:223537772-223538667	H1-hESC	embryonic stem cell:	n/a	n/a
20	SIN3A	chr1:223537894-223538791	H1-hESC	embryonic stem cell:	n/a	chr1:223537953-223537964
21	CCNT2	chr1:223537418-223538160	K562	blood:	n/a	n/a
22	MAX	chr1:223537564-223538102	ECC-1	luminal epithelium:	n/a	n/a
23	RAD21	chr1:223537769-223538262	H1-hESC	embryonic stem cell:	n/a	n/a
24	E2F6	chr1:223537703-223538550	H1-hESC	embryonic stem cell:	n/a	chr1:223538169-223538176 chr1:223538169-223538176 chr1:223538169-223538176 chr1:223538386-223538395 chr1:223538386-223538398 chr1:223538394-223538403
25	BACH1	chr1:223537905-223538237	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223536038..223539069-chr1:223546089..223550790,4	MCF-7	breast:
2	chr1:223305860..223308306-chr1:223535536..223539484,5	MCF-7	breast:

Variant related genes	Relation type
SUSD4	TF binding region
ENSG00000187554	Chromatin interaction
ENSG00000251789	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10495206	0.83[EUR][1000 genomes]
rs10495207	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10907376	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11261264	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11261270	0.84[EUR][1000 genomes]
rs12123148	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12140453	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12564615	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1547788	0.83[EUR][1000 genomes]
rs1619227	0.86[EUR][1000 genomes]
rs17162008	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17163827	0.83[EUR][1000 genomes]
rs17163831	0.82[EUR][1000 genomes]
rs17480087	0.83[EUR][1000 genomes]
rs17480344	0.83[EUR][1000 genomes]
rs17539269	0.83[EUR][1000 genomes]
rs17539583	0.83[EUR][1000 genomes]
rs17578168	0.83[EUR][1000 genomes]
rs17578203	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1772280	0.92[EUR][1000 genomes]
rs2138966	0.83[EUR][1000 genomes]
rs34150324	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59355120	0.85[EUR][1000 genomes]
rs61838210	0.83[EUR][1000 genomes]
rs61838229	0.83[EUR][1000 genomes]
rs61838230	0.82[EUR][1000 genomes]
rs61838231	0.82[EUR][1000 genomes]
rs61838238	0.83[EUR][1000 genomes]
rs61838239	0.83[EUR][1000 genomes]
rs61838240	0.83[EUR][1000 genomes]
rs61838243	0.83[EUR][1000 genomes]
rs61838250	0.86[EUR][1000 genomes]
rs61839867	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61839875	0.84[EUR][1000 genomes]
rs61839876	0.85[EUR][1000 genomes]
rs61839877	0.84[EUR][1000 genomes]
rs61839878	0.84[EUR][1000 genomes]
rs61839879	0.85[EUR][1000 genomes]
rs6604709	0.86[EUR][1000 genomes]
rs7555607	0.86[EUR][1000 genomes]
rs870486	0.80[EUR][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	nsv1010798	chr1:223498145-223538989	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv826809	chr1:223536032-223538665	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	esv3438398	chr1:223536354-223539202	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	esv3412152	chr1:223536929-223539252	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61838252	SUSD4	cis	Heart Left Ventricle	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223535800-223538200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:223535800-223538800	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr1:223535800-223538800	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr1:223535800-223538800	Active TSS	Ovary	ovary
5	chr1:223535800-223539000	Active TSS	Brain Anterior Caudate	brain
6	chr1:223536000-223538200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
7	chr1:223536000-223538400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
8	chr1:223536000-223538600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr1:223536000-223538600	Active TSS	Brain Hippocampus Middle	brain
10	chr1:223536200-223538600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr1:223536200-223538800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr1:223536200-223538800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr1:223536200-223539000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr1:223536200-223539000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:223536200-223539000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
16	chr1:223536400-223538000	Active TSS	HSMMtube	muscle
17	chr1:223536400-223538200	Bivalent/Poised TSS	NHLF	lung
18	chr1:223536400-223538600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:223536600-223538200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr1:223536600-223538200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:223536600-223538200	Active TSS	Brain Substantia Nigra	brain
22	chr1:223536600-223538200	Bivalent Enhancer	Spleen	Spleen
23	chr1:223536600-223538400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:223536600-223538400	Active TSS	Brain Cingulate Gyrus	brain
25	chr1:223536600-223538400	Active TSS	Fetal Heart	heart
26	chr1:223536600-223538600	Active TSS	H9 Cell Line	embryonic stem cell
27	chr1:223536600-223538600	Active TSS	Gastric	stomach
28	chr1:223536800-223538200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:223536800-223538200	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr1:223536800-223538200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:223536800-223538200	Active TSS	Aorta	Aorta
32	chr1:223536800-223538200	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
33	chr1:223536800-223538200	Bivalent/Poised TSS	Fetal Brain Female	brain
34	chr1:223536800-223538200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
35	chr1:223536800-223538200	Active TSS	Left Ventricle	heart
36	chr1:223536800-223538200	Bivalent/Poised TSS	HepG2	liver
37	chr1:223536800-223538600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:223536800-223538600	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr1:223536800-223538600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:223536800-223538600	Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr1:223536800-223538600	Active TSS	Rectal Smooth Muscle	rectum
42	chr1:223536800-223538800	Active TSS	Brain Angular Gyrus	brain
43	chr1:223537000-223538000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:223537000-223538000	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:223537000-223538200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr1:223537000-223538200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:223537000-223538200	Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr1:223537000-223538200	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr1:223537000-223538200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr1:223537000-223538400	Active TSS	Primary T cells from cord blood	blood

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