Variant report

Variant	rs3811019
Chromosome Location	chr1:114471583-114471584
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:222)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:222 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:114470792-114473521	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:114470836-114473396	K562	blood:	n/a	n/a
3	MAFF	chr1:114471544-114471958	K562	blood:	n/a	n/a
4	CREB1	chr1:114471417-114472791	K562	blood:	n/a	n/a
5	E2F4	chr1:114471562-114471767	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr1:114471457-114472447	U87	brain:	n/a	n/a
7	POLR2A	chr1:114471482-114473538	H1-neurons	neurons:	n/a	n/a
8	POLR2A	chr1:114471073-114473562	GM12878	blood:	n/a	n/a
9	MXI1	chr1:114470648-114473883	SK-N-SH	brain:	n/a	n/a
10	ATF2	chr1:114471304-114472317	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:114471538-114473494	K562	blood:	n/a	n/a
12	POLR2A	chr1:114471293-114473102	GM18526	blood:	n/a	n/a
13	ELF1	chr1:114471516-114473429	K562	blood:	n/a	chr1:114472196-114472208 chr1:114472308-114472320
14	MAX	chr1:114471557-114472450	A549	lung:	n/a	n/a
15	MAFK	chr1:114470700-114472281	K562	blood:	n/a	n/a
16	CHD1	chr1:114471119-114472254	GM12878	blood:	n/a	chr1:114472166-114472176
17	ZNF143	chr1:114471389-114472959	GM12878	blood:	n/a	chr1:114472703-114472713
18	GTF2F1	chr1:114471537-114472322	K562	blood:	n/a	n/a
19	BHLHE40	chr1:114471510-114472328	HepG2	liver:	n/a	chr1:114472288-114472304 chr1:114472299-114472315
20	SIN3A	chr1:114471570-114473630	H1-hESC	embryonic stem cell:	n/a	chr1:114472939-114472947 chr1:114472289-114472302
21	MXI1	chr1:114471415-114473383	HepG2	liver:	n/a	n/a
22	TEAD4	chr1:114471328-114472330	K562	blood:	n/a	n/a
23	MAFK	chr1:114471494-114472302	Hela-S3	cervix:	n/a	n/a
24	MAZ	chr1:114471330-114474073	IMR90	lung:	n/a	chr1:114472800-114472810 chr1:114473592-114473601
25	POLR2A	chr1:114471568-114473374	Hela-S3	cervix:	n/a	n/a
26	YY1	chr1:114471477-114472859	GM12892	blood:	n/a	chr1:114472195-114472209 chr1:114472519-114472530 chr1:114472663-114472677 chr1:114472259-114472270 chr1:114472476-114472490
27	ZNF384	chr1:114471388-114471622	GM12878	blood:	n/a	n/a
28	GABPA	chr1:114470713-114473802	MCF-7	breast:	n/a	chr1:114472320-114472329
29	TBL1XR1	chr1:114470882-114472320	GM12878	blood:	n/a	n/a
30	FOXA2	chr1:114471487-114472091	A549	lung:	n/a	n/a
31	HEY1	chr1:114471146-114472447	HepG2	liver:	n/a	chr1:114472277-114472292
32	POLR2A	chr1:114470824-114473119	Raji	blood:	n/a	n/a
33	ZNF143	chr1:114471566-114472357	K562	blood:	n/a	n/a
34	SMARCC1	chr1:114471417-114473585	Hela-S3	cervix:	n/a	n/a
35	GABPA	chr1:114471528-114472394	SK-N-SH	brain:	n/a	chr1:114472320-114472329
36	TBP	chr1:114470891-114473736	K562	blood:	n/a	n/a
37	POLR2A	chr1:114471582-114472515	PFSK-1	brain:	n/a	n/a
38	RFX5	chr1:114471394-114472304	HepG2	liver:	n/a	n/a
39	FOXA2	chr1:114471529-114471954	A549	lung:	n/a	n/a
40	RUNX3	chr1:114470721-114472371	GM12878	blood:	n/a	n/a
41	POLR2A	chr1:114470968-114472954	HepG2	liver:	n/a	n/a
42	MBD4	chr1:114471328-114472248	HepG2	liver:	n/a	n/a
43	POLR2A	chr1:114470515-114473570	K562	blood:	n/a	n/a
44	POLR2A	chr1:114471398-114472369	HepG2	liver:	n/a	n/a
45	TBP	chr1:114470932-114472285	GM12878	blood:	n/a	n/a
46	NFIC	chr1:114471574-114472291	GM12878	blood:	n/a	n/a
47	RELA	chr1:114471271-114472354	GM18951	blood:	n/a	n/a
48	CHD1	chr1:114471322-114475053	IMR90	lung:	n/a	chr1:114472166-114472176
49	PML	chr1:114471482-114473795	K562	blood:	n/a	n/a
50	HNF4G	chr1:114471472-114471870	HepG2	liver:	n/a	chr1:114471657-114471672

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114471153..114473640-chr17:59476771..59478545,2	MCF-7	breast:
2	chr1:114377772..114378781-chr1:114470981..114471810,3	MCF-7	breast:
3	chr1:108289707..108293879-chr1:114470865..114473423,4	MCF-7	breast:
4	chr1:114447452..114448400-chr1:114471566..114472757,4	Hela-S3	cervix:
5	chr1:114471318..114473682-chr17:59475992..59478676,2	MCF-7	breast:
6	chr1:114353086..114356383-chr1:114467552..114475359,15	MCF-7	breast:
7	chr1:114299235..114302663-chr1:114470274..114473459,3	K562	blood:
8	chr1:114300069..114302951-chr1:114469985..114474355,4	MCF-7	breast:
9	chr1:114351760..114356326-chr1:114471041..114474785,9	K562	blood:
10	chr1:114444168..114452207-chr1:114466193..114476714,61	K562	blood:
11	chr1:114469554..114476691-chr1:114493097..114498363,7	MCF-7	breast:
12	chr1:114447178..114448996-chr1:114471115..114472973,22	MCF-7	breast:
13	chr1:114300200..114301915-chr1:114470901..114473894,2	MCF-7	breast:
14	chr1:108741161..108744200-chr1:114469971..114473274,3	MCF-7	breast:
15	chr1:114447369..114448385-chr1:114471257..114473158,18	MCF-7	breast:
16	chr1:114352160..114355349-chr1:114470537..114474785,4	K562	blood:
17	chr1:114470673..114473075-chr16:450178..453136,2	MCF-7	breast:
18	chr1:114439933..114443921-chr1:114470851..114474658,5	K562	blood:
19	chr1:114352067..114356642-chr1:114470131..114477025,16	MCF-7	breast:
20	chr1:114471506..114473104-chr1:114522240..114523784,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AP4B1-1	chr1:114471325-114471880	ENSG00000235527
2	lnc-AP4B1-1	chr1:114470866-114471854	ENSG00000235527

No data

Variant related genes	Relation type
HIPK1	TF binding region
ENSG00000267131	Chromatin interaction
ENSG00000134262	Chromatin interaction
ENSG00000118655	Chromatin interaction
ENSG00000134215	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000231128	Chromatin interaction
ENSG00000242612	Chromatin interaction
ENSG00000085491	Chromatin interaction
ENSG00000081019	Chromatin interaction
ENSG00000116793	Chromatin interaction
ENSG00000116774	Chromatin interaction
ENSG00000260879	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs17032011	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS 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 target site	96 gene(s)	inside rSNPs	diseases
2	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	esv3349186	chr1:114471379-114473627	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3811019	SMTN	trans	brain	seeQTL
rs3811019	PTPN22	cis	parietal	SCAN
rs3811019	MAGI3	cis	cerebellum	SCAN
rs3811019	SYT6	cis	parietal	SCAN
rs3811019	PHTF1	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114470400-114471600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:114470600-114471600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:114470600-114471800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr1:114470800-114471600	Flanking Active TSS	Brain Anterior Caudate	brain
5	chr1:114470800-114471600	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr1:114470800-114471600	Active TSS	Fetal Brain Male	brain
7	chr1:114470800-114471600	Flanking Active TSS	Fetal Kidney	kidney
8	chr1:114470800-114471600	Flanking Active TSS	Fetal Stomach	stomach
9	chr1:114470800-114471600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
10	chr1:114470800-114471600	Flanking Active TSS	Rectal Smooth Muscle	rectum
11	chr1:114470800-114471600	Flanking Active TSS	NH-A	brain
12	chr1:114470800-114471600	Flanking Active TSS	NHEK	skin
13	chr1:114470800-114471600	Flanking Active TSS	Osteobl	bone
14	chr1:114470800-114471800	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr1:114470800-114471800	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr1:114470800-114471800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:114470800-114471800	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr1:114470800-114471800	Flanking Active TSS	Hela-S3	cervix
19	chr1:114470800-114471800	Flanking Active TSS	HMEC	breast
20	chr1:114470800-114472000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:114470800-114472000	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr1:114470800-114473400	Active TSS	Fetal Intestine Large	intestine
23	chr1:114470800-114473400	Active TSS	Fetal Intestine Small	intestine
24	chr1:114470800-114474000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:114470800-114474200	Active TSS	Aorta	Aorta
26	chr1:114470800-114476200	Active TSS	Thymus	Thymus
27	chr1:114471000-114471600	Flanking Active TSS	Primary B cells from peripheral blood	blood
28	chr1:114471000-114471600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr1:114471000-114471600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr1:114471000-114471600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:114471000-114471600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
32	chr1:114471000-114471600	Flanking Active TSS	Brain Substantia Nigra	brain
33	chr1:114471000-114471600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr1:114471000-114471600	Flanking Active TSS	Fetal Thymus	thymus
35	chr1:114471000-114471600	Flanking Active TSS	Dnd41	blood
36	chr1:114471000-114471800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr1:114471000-114471800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr1:114471000-114471800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr1:114471000-114471800	Flanking Active TSS	Fetal Muscle Leg	muscle
40	chr1:114471000-114471800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr1:114471000-114472000	Active TSS	Right Atrium	heart
42	chr1:114471000-114472600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:114471000-114473000	Active TSS	Placenta	Placenta
44	chr1:114471000-114473000	Active TSS	Right Ventricle	heart
45	chr1:114471000-114473200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:114471000-114473200	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr1:114471000-114473400	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr1:114471000-114473400	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr1:114471000-114473400	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr1:114471000-114473400	Active TSS	Stomach Mucosa	stomach

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