Variant report

Variant	rs4411917
Chromosome Location	chr3:119421427-119421428
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	SP1	chr3:119421184-119422129	H1-hESC	embryonic stem cell:	n/a	chr3:119421531-119421545 chr3:119421549-119421558 chr3:119421539-119421553 chr3:119421544-119421558 chr3:119421548-119421557 chr3:119421543-119421553 chr3:119421543-119421552 chr3:119421542-119421554 chr3:119421549-119421558 chr3:119421544-119421553 chr3:119421655-119421669 chr3:119421547-119421559 chr3:119421542-119421554
2	MXI1	chr3:119421136-119423363	SK-N-SH	brain:	n/a	n/a
3	JUND	chr3:119421343-119422149	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZNF143	chr3:119421391-119422020	H1-hESC	embryonic stem cell:	n/a	chr3:119421538-119421556
5	POLR2A	chr3:119421413-119422002	U87	brain:	n/a	n/a
6	POLR2A	chr3:119421402-119422053	SK-N-SH	brain:	n/a	n/a
7	MAZ	chr3:119421350-119422533	IMR90	lung:	n/a	n/a
8	HDAC2	chr3:119421353-119421675	H1-hESC	embryonic stem cell:	n/a	n/a
9	RELA	chr3:119421346-119421927	GM18951	blood:	n/a	n/a
10	TAF1	chr3:119421361-119421796	H1-hESC	embryonic stem cell:	n/a	n/a
11	TCF12	chr3:119421416-119422113	ECC-1	luminal epithelium:	n/a	n/a
12	NR2F2	chr3:119421412-119422087	MCF-7	breast:	n/a	n/a
13	MAX	chr3:119421387-119422207	SK-N-SH	brain:	n/a	n/a
14	REST	chr3:119421254-119422386	H1-neurons	neurons:	n/a	chr3:119422137-119422150 chr3:119422199-119422208
15	MAX	chr3:119421256-119422379	H1-hESC	embryonic stem cell:	n/a	n/a
16	SP1	chr3:119421214-119422066	A549	lung:	n/a	chr3:119421531-119421545 chr3:119421549-119421558 chr3:119421539-119421553 chr3:119421544-119421558 chr3:119421548-119421557 chr3:119421543-119421553 chr3:119421543-119421552 chr3:119421542-119421554 chr3:119421549-119421558 chr3:119421544-119421553 chr3:119421655-119421669 chr3:119421547-119421559 chr3:119421542-119421554
17	BACH1	chr3:119421256-119421985	H1-hESC	embryonic stem cell:	n/a	n/a
18	SP1	chr3:119421194-119422002	H1-hESC	embryonic stem cell:	n/a	chr3:119421531-119421545 chr3:119421549-119421558 chr3:119421539-119421553 chr3:119421544-119421558 chr3:119421548-119421557 chr3:119421543-119421553 chr3:119421543-119421552 chr3:119421542-119421554 chr3:119421549-119421558 chr3:119421544-119421553 chr3:119421655-119421669 chr3:119421547-119421559 chr3:119421542-119421554
19	MTA3	chr3:119421270-119421852	GM12878	blood:	n/a	n/a
20	TBP	chr3:119421418-119421985	H1-hESC	embryonic stem cell:	n/a	n/a
21	MXI1	chr3:119421213-119422295	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
MAATS1	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10934497	0.85[AMR][1000 genomes]
rs12721613	1.00[MEX][hapmap]
rs1523128	1.00[MEX][hapmap]
rs1523129	1.00[MEX][hapmap]
rs2472668	1.00[MEX][hapmap]
rs2688635	1.00[MEX][hapmap]
rs2688643	1.00[MEX][hapmap]
rs2692619	1.00[MEX][hapmap]
rs4234663	0.87[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4234665	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4355316	0.87[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4579049	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4687878	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4687879	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4687880	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4687883	1.00[MEX][hapmap]
rs4688038	1.00[MEX][hapmap]
rs6438543	0.87[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6438544	0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6792664	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7624672	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7624768	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs940087	1.00[MEX][hapmap]
rs9816750	1.00[MEX][hapmap]
rs9834908	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9838456	1.00[MEX][hapmap]

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	nsv460834	chr3:119384163-119458851	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv591390	chr3:119384163-119458851	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv591391	chr3:119403145-119442572	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119418400-119422200	ZNF genes & repeats	GM12878-XiMat	blood
2	chr3:119421000-119421800	Enhancers	Spleen	Spleen
3	chr3:119421200-119421600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:119421200-119421600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:119421200-119421600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:119421200-119421600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr3:119421200-119421600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr3:119421200-119421600	Enhancers	Primary hematopoietic stem cells	blood
9	chr3:119421200-119421600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
10	chr3:119421200-119421600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:119421200-119421600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:119421200-119421600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:119421200-119421600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:119421200-119421600	Flanking Active TSS	Brain Cingulate Gyrus	brain
15	chr3:119421200-119421600	Flanking Active TSS	Brain Hippocampus Middle	brain
16	chr3:119421200-119421600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr3:119421200-119421600	Flanking Active TSS	Fetal Brain Female	brain
18	chr3:119421200-119421600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
19	chr3:119421200-119421600	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr3:119421200-119421600	Flanking Active TSS	HSMMtube	muscle
21	chr3:119421200-119421600	Flanking Active TSS	HUVEC	blood vessel
22	chr3:119421200-119421600	Flanking Active TSS	NH-A	brain
23	chr3:119421200-119421600	Flanking Active TSS	Osteobl	bone
24	chr3:119421200-119421800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr3:119421200-119421800	Flanking Active TSS	HMEC	breast
26	chr3:119421200-119421800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr3:119421200-119422000	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr3:119421200-119422000	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr3:119421200-119422000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:119421200-119422000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:119421200-119422000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:119421200-119422000	Active TSS	Muscle Satellite Cultured Cells	--
33	chr3:119421200-119422000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:119421200-119422000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:119421200-119422000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:119421200-119422000	Active TSS	Aorta	Aorta
37	chr3:119421200-119422000	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr3:119421200-119422000	Active TSS	Right Ventricle	heart
39	chr3:119421200-119422200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr3:119421200-119422200	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr3:119421200-119422200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr3:119421200-119422200	Active TSS	Brain Substantia Nigra	brain
43	chr3:119421200-119422200	Active TSS	Rectal Smooth Muscle	rectum
44	chr3:119421200-119422200	Flanking Active TSS	A549	lung
45	chr3:119421200-119422200	Active TSS	NHDF-Ad	bronchial
46	chr3:119421200-119422400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr3:119421200-119422400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:119421200-119422400	Active TSS	Brain Angular Gyrus	brain
49	chr3:119421200-119422400	Active TSS	Colon Smooth Muscle	Colon
50	chr3:119421200-119422400	Flanking Active TSS	Duodenum Mucosa	Duodenum

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