Variant report

Variant	rs9811460
Chromosome Location	chr3:49210904-49210905
allele	A/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	NFIC	chr3:49210685-49211332	SK-N-SH	brain:	n/a	chr3:49210992-49211008 chr3:49210921-49210938
2	MEF2A	chr3:49210715-49211082	K562	blood:	n/a	chr3:49210883-49210898 chr3:49210883-49210899 chr3:49210883-49210898 chr3:49210885-49210896 chr3:49210879-49210900 chr3:49210886-49210895 chr3:49210882-49210898
3	REST	chr3:49210812-49211590	SK-N-SH	brain:	n/a	n/a
4	REST	chr3:49210427-49211993	H1-neurons	neurons:	n/a	n/a
5	CHD2	chr3:49210879-49211054	K562	blood:	n/a	n/a
6	POLR2A	chr3:49210676-49211201	H1-neurons	neurons:	n/a	n/a
7	MEF2A	chr3:49210626-49211078	K562	blood:	n/a	chr3:49210627-49210635 chr3:49210883-49210898 chr3:49210883-49210899 chr3:49210883-49210898 chr3:49210885-49210896 chr3:49210879-49210900 chr3:49210886-49210895 chr3:49210882-49210898
8	MXI1	chr3:49208067-49212337	SK-N-SH	brain:	n/a	chr3:49211019-49211034 chr3:49211021-49211036
9	POLR2A	chr3:49210721-49211608	H1-neurons	neurons:	n/a	n/a
10	SIN3A	chr3:49210883-49211255	H1-hESC	embryonic stem cell:	n/a	n/a
11	NFIC	chr3:49210601-49211651	SK-N-SH	brain:	n/a	chr3:49210992-49211008 chr3:49210921-49210938
12	REST	chr3:49210847-49211104	K562	blood:	n/a	n/a
13	GATA2	chr3:49210851-49211655	SH-SY5Y	brain:	n/a	chr3:49211039-49211046 chr3:49211080-49211087
14	TBL1XR1	chr3:49210624-49211122	K562	blood:	n/a	n/a
15	ATF1	chr3:49210851-49211145	K562	blood:	n/a	n/a
16	POLR2A	chr3:49210904-49210914	K562	blood:	n/a	n/a
17	EP300	chr3:49210750-49211254	SK-N-SH_RA	brain:	n/a	n/a
18	SRF	chr3:49210880-49211079	HepG2	liver:	n/a	n/a
19	REST	chr3:49210894-49211035	K562	blood:	n/a	n/a
20	RCOR1	chr3:49210776-49211213	K562	blood:	n/a	n/a
21	RAD21	chr3:49210791-49211644	SK-N-SH_RA	brain:	n/a	chr3:49211373-49211386 chr3:49211355-49211364
22	ZMIZ1	chr3:49210797-49210910	K562	blood:	n/a	n/a
23	GATA1	chr3:49210850-49211596	PBDE	blood:	n/a	chr3:49211039-49211046 chr3:49211080-49211087
24	JUND	chr3:49210900-49211033	H1-hESC	embryonic stem cell:	n/a	n/a
25	EP300	chr3:49210783-49211182	K562	blood:	n/a	n/a
26	JUND	chr3:49210839-49211150	K562	blood:	n/a	n/a
27	USF1	chr3:49210838-49211212	SK-N-SH_RA	brain:	n/a	n/a
28	POLR2A	chr3:49210849-49211158	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr3:49210846-49211098	K562	blood:	n/a	n/a
30	SP1	chr3:49210801-49211194	H1-hESC	embryonic stem cell:	n/a	chr3:49210952-49210961 chr3:49210952-49210966 chr3:49210951-49210962 chr3:49210952-49210962 chr3:49210953-49210962 chr3:49210952-49210962
31	NR2F2	chr3:49210558-49211119	K562	blood:	n/a	n/a
32	USF1	chr3:49210863-49211126	SK-N-SH_RA	brain:	n/a	n/a
33	ZBTB7A	chr3:49210857-49211053	K562	blood:	n/a	n/a
34	MYC	chr3:49210870-49210943	K562	blood:	n/a	n/a
35	MYC	chr3:49210863-49211110	K562	blood:	n/a	chr3:49211021-49211030
36	MAZ	chr3:49210763-49211124	K562	blood:	n/a	chr3:49211021-49211030
37	NFIC	chr3:49210869-49211108	HepG2	liver:	n/a	chr3:49210992-49211008 chr3:49210921-49210938
38	EP300	chr3:49210709-49211171	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49207667..49210496-chr3:49210545..49213014,4	K562	blood:
2	chr3:49195402..49201533-chr3:49207296..49212401,9	MCF-7	breast:
3	chr3:49156732..49159393-chr3:49207552..49211410,3	K562	blood:

Variant related genes	Relation type
KLHDC8B	TF binding region
ENSG00000172037	Chromatin interaction
ENSG00000270441	Chromatin interaction
ENSG00000172046	Chromatin interaction
ENSG00000185909	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11717485	1.00[EUR][1000 genomes]
rs13318132	1.00[EUR][1000 genomes]
rs14828	1.00[EUR][1000 genomes]
rs1522929	1.00[EUR][1000 genomes]
rs17080495	1.00[EUR][1000 genomes]
rs17080510	1.00[EUR][1000 genomes]
rs17080567	1.00[EUR][1000 genomes]
rs1996874	1.00[EUR][1000 genomes]
rs28615670	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4452334	1.00[EUR][1000 genomes]
rs4527417	1.00[EUR][1000 genomes]
rs4855872	1.00[EUR][1000 genomes]
rs4855874	1.00[EUR][1000 genomes]
rs4855875	1.00[EUR][1000 genomes]
rs4855876	1.00[EUR][1000 genomes]
rs4855878	1.00[EUR][1000 genomes]
rs4855879	1.00[EUR][1000 genomes]
rs55990645	1.00[EUR][1000 genomes]
rs56101322	1.00[EUR][1000 genomes]
rs56760510	1.00[EUR][1000 genomes]
rs56897974	1.00[EUR][1000 genomes]
rs58914641	1.00[EUR][1000 genomes]
rs58998762	1.00[EUR][1000 genomes]
rs60011446	1.00[EUR][1000 genomes]
rs60338814	1.00[EUR][1000 genomes]
rs61008775	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61744082	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61749312	1.00[EUR][1000 genomes]
rs6446270	1.00[EUR][1000 genomes]
rs6446271	1.00[EUR][1000 genomes]
rs6446273	1.00[EUR][1000 genomes]
rs6446276	1.00[EUR][1000 genomes]
rs6766297	1.00[EUR][1000 genomes]
rs6787665	1.00[EUR][1000 genomes]
rs6793124	1.00[EUR][1000 genomes]
rs72930094	1.00[EUR][1000 genomes]
rs72931171	1.00[EUR][1000 genomes]
rs72934791	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72936804	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72936810	1.00[EUR][1000 genomes]
rs72936890	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830703	1.00[EUR][1000 genomes]
rs73830704	1.00[EUR][1000 genomes]
rs73830705	1.00[EUR][1000 genomes]
rs73830706	1.00[EUR][1000 genomes]
rs73833525	1.00[EUR][1000 genomes]
rs8179172	1.00[EUR][1000 genomes]
rs9814413	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9820609	1.00[EUR][1000 genomes]
rs9833422	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9837396	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9849446	1.00[EUR][1000 genomes]
rs9861805	1.00[EUR][1000 genomes]
rs9869504	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9875203	1.00[EUR][1000 genomes]
rs9877045	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9882714	1.00[EUR][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	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49208200-49211200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:49208200-49211400	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr3:49208200-49212000	Flanking Active TSS	Brain Germinal Matrix	brain
4	chr3:49209200-49211800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:49209200-49212000	Flanking Active TSS	Fetal Brain Female	brain
6	chr3:49209200-49212400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:49209400-49211200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr3:49209400-49211200	Flanking Active TSS	K562	blood
9	chr3:49209400-49211400	Flanking Active TSS	HepG2	liver
10	chr3:49209400-49211600	Flanking Active TSS	Fetal Lung	lung
11	chr3:49209400-49211600	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr3:49209600-49211000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr3:49209600-49211000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr3:49209600-49211200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:49209600-49211400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:49209600-49211400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:49209600-49211400	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr3:49209600-49211600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:49209600-49211600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
20	chr3:49209600-49211800	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
21	chr3:49209600-49211800	Flanking Active TSS	HSMMtube	muscle
22	chr3:49209600-49212000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:49209600-49212000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
24	chr3:49209600-49213800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr3:49209800-49211200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:49209800-49211200	Enhancers	Placenta Amnion	Placenta Amnion
27	chr3:49209800-49211200	Flanking Active TSS	HSMM	muscle
28	chr3:49209800-49211400	Flanking Active TSS	Left Ventricle	heart
29	chr3:49209800-49211400	Flanking Active TSS	Right Ventricle	heart
30	chr3:49209800-49212000	Enhancers	H1 Cell Line	embryonic stem cell
31	chr3:49209800-49212400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:49209800-49212600	Enhancers	Fetal Brain Male	brain
33	chr3:49209800-49215000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr3:49210000-49211000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr3:49210000-49211200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:49210000-49211200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:49210000-49211400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr3:49210000-49211400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
39	chr3:49210000-49211400	Enhancers	Brain Substantia Nigra	brain
40	chr3:49210000-49211600	Weak transcription	Primary T cells from cord blood	blood
41	chr3:49210000-49211600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:49210000-49211600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr3:49210000-49211600	Flanking Active TSS	Rectal Smooth Muscle	rectum
44	chr3:49210000-49211600	Flanking Active TSS	Right Atrium	heart
45	chr3:49210000-49211800	Flanking Active TSS	Fetal Intestine Large	intestine
46	chr3:49210000-49211800	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
47	chr3:49210000-49211800	Enhancers	Placenta	Placenta
48	chr3:49210000-49211800	Flanking Active TSS	Ovary	ovary
49	chr3:49210000-49212000	Enhancers	Osteobl	bone
50	chr3:49210000-49212800	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland

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