Variant report

Variant	rs2198199
Chromosome Location	chr4:103789782-103789783
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	RCOR1	chr4:103789719-103790721	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:103789659-103790869	HUVEC	blood vessel:	n/a	n/a
3	RFX5	chr4:103789772-103790264	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr4:103789260-103791495	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr4:103789516-103791189	MCF10A-Er-Src	breast:	n/a	n/a
6	SP1	chr4:103789637-103790732	A549	lung:	n/a	chr4:103789825-103789837 chr4:103790072-103790093 chr4:103790420-103790434 chr4:103789825-103789837 chr4:103790423-103790434 chr4:103790423-103790435 chr4:103790423-103790435 chr4:103789822-103789836 chr4:103790425-103790434 chr4:103789827-103789836
7	POLR2A	chr4:103789742-103790951	H1-neurons	neurons:	n/a	n/a
8	SETDB1	chr4:103789774-103790742	U2OS	brain:	n/a	chr4:103790176-103790185
9	POLR2A	chr4:103789434-103791480	IMR90	lung:	n/a	n/a
10	E2F6	chr4:103789685-103790861	K562	blood:	n/a	chr4:103790068-103790080 chr4:103790025-103790036 chr4:103790068-103790077 chr4:103790178-103790188 chr4:103790176-103790185
11	CREB1	chr4:103789588-103790980	HepG2	liver:	n/a	n/a
12	CREB1	chr4:103789686-103790975	HepG2	liver:	n/a	n/a
13	USF1	chr4:103789680-103791011	HCT-116	colon:	n/a	chr4:103790449-103790458 chr4:103790923-103790939 chr4:103790447-103790460 chr4:103790449-103790458 chr4:103790167-103790183 chr4:103790448-103790457 chr4:103790448-103790459
14	POLR2A	chr4:103789762-103790800	MCF-7	breast:	n/a	n/a
15	TAF1	chr4:103789782-103790668	HepG2	liver:	n/a	n/a
16	BCLAF1	chr4:103789522-103790938	GM12878	blood:	n/a	chr4:103789561-103789570 chr4:103790925-103790938 chr4:103790183-103790196
17	POLR2A	chr4:103789780-103790725	HUVEC	blood vessel:	n/a	n/a
18	RELA	chr4:103789552-103791216	GM18505	blood:	n/a	n/a
19	GTF2F1	chr4:103789709-103790853	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr4:103789668-103791323	H1-hESC	embryonic stem cell:	n/a	n/a
21	HA-E2F1	chr4:103789657-103790910	MCF-7	breast:	n/a	chr4:103790068-103790077 chr4:103790178-103790188 chr4:103790176-103790185
22	CEBPB	chr4:103789740-103789968	K562	blood:	n/a	n/a
23	REST	chr4:103789610-103790086	A549	lung:	n/a	n/a
24	E2F4	chr4:103789696-103790656	MCF10A-Er-Src	breast:	n/a	chr4:103790068-103790080 chr4:103790068-103790077 chr4:103790178-103790188 chr4:103790176-103790185 chr4:103790025-103790036
25	YY1	chr4:103789649-103790742	GM12878	blood:	n/a	chr4:103790068-103790077 chr4:103790065-103790076 chr4:103790169-103790183
26	TAF1	chr4:103789641-103790815	K562	blood:	n/a	n/a
27	RELA	chr4:103789661-103790855	GM15510	blood:	n/a	n/a
28	CHD1	chr4:103789528-103789926	H1-hESC	embryonic stem cell:	n/a	n/a
29	TEAD4	chr4:103789359-103791151	K562	blood:	n/a	n/a
30	POLR2A	chr4:103789660-103790821	GM12892	blood:	n/a	n/a
31	TEAD4	chr4:103789756-103790619	H1-hESC	embryonic stem cell:	n/a	n/a
32	CBX3	chr4:103789717-103790091	K562	blood:	n/a	n/a
33	MYC	chr4:103789431-103791158	K562	blood:	n/a	chr4:103790444-103790463 chr4:103790451-103790467
34	HMGN3	chr4:103789769-103790669	K562	blood:	n/a	n/a
35	PML	chr4:103789773-103790105	GM12878	blood:	n/a	n/a
36	HEY1	chr4:103789661-103790880	HepG2	liver:	n/a	chr4:103790173-103790188
37	POLR2A	chr4:103789721-103790861	HepG2	liver:	n/a	n/a
38	POLR2A	chr4:103789646-103791220	K562	blood:	n/a	n/a
39	POLR2A	chr4:103789722-103790948	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAX	chr4:103789685-103790985	H1-hESC	embryonic stem cell:	n/a	chr4:103790444-103790463 chr4:103790451-103790467
41	CEBPD	chr4:103789627-103791264	K562	blood:	n/a	chr4:103790834-103790845
42	POLR2A	chr4:103789557-103790832	Gliobla	brain:	n/a	n/a
43	POLR2A	chr4:103789305-103791046	GM12878	blood:	n/a	n/a
44	ATF2	chr4:103789692-103791226	GM12878	blood:	n/a	n/a
45	MAX	chr4:103789608-103790994	H1-hESC	embryonic stem cell:	n/a	chr4:103790444-103790463 chr4:103790451-103790467
46	IRF1	chr4:103789533-103793235	K562	blood:	n/a	chr4:103792312-103792322 chr4:103789825-103789839 chr4:103792396-103792407 chr4:103792306-103792326 chr4:103789561-103789575 chr4:103792312-103792326 chr4:103789560-103789569 chr4:103792311-103792325 chr4:103790423-103790437 chr4:103789927-103789940 chr4:103792311-103792325 chr4:103792312-103792325 chr4:103792394-103792408
47	USF1	chr4:103789770-103790738	H1-hESC	embryonic stem cell:	n/a	chr4:103790449-103790458 chr4:103790447-103790460 chr4:103790449-103790458 chr4:103790167-103790183 chr4:103790448-103790457 chr4:103790448-103790459
48	RUNX3	chr4:103789517-103791158	GM12878	blood:	n/a	n/a
49	TEAD4	chr4:103789697-103790801	ECC-1	luminal epithelium:	n/a	n/a
50	MXI1	chr4:103789737-103790884	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:103746553..103755574-chr4:103787108..103794302,29	MCF-7	breast:
2	chr4:103745482..103752084-chr4:103788371..103792114,20	MCF-7	breast:
3	chr4:103741330..103752134-chr4:103778393..103796398,92	K562	blood:
4	chr4:103782723..103785636-chr4:103787155..103789919,2	MCF-7	breast:
5	chr10:65280457..65281194-chr4:103789505..103790213,2	HCT-116	colon:
6	chr4:103757981..103760210-chr4:103788779..103792058,4	MCF-7	breast:
7	chr4:103420299..103423075-chr4:103789443..103791523,3	K562	blood:
8	chr4:103789205..103791017-chr4:103995982..103997960,2	K562	blood:
9	chr21:40751768..40752544-chr4:103789675..103790558,3	Hela-S3	cervix:
10	chr4:103420801..103422713-chr4:103788549..103790211,2	MCF-7	breast:
11	chr4:103736995..103756245-chr4:103778393..103800311,117	K562	blood:
12	chr2:86849205..86851980-chr4:103788532..103791480,2	MCF-7	breast:
13	chr4:103421575..103424271-chr4:103788743..103790943,2	K562	blood:
14	chr4:103775426..103778667-chr4:103788378..103789993,3	MCF-7	breast:

Variant related genes	Relation type
CISD2	TF binding region
ENSG00000252739	Chromatin interaction
ENSG00000109320	Chromatin interaction
ENSG00000260651	Chromatin interaction
ENSG00000246560	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000165476	Chromatin interaction
ENSG00000249884	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000164038	Chromatin interaction
ENSG00000239305	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10005010	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap]
rs10025625	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10033243	0.83[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs1383732	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap]
rs17033384	0.89[ASW][hapmap];0.83[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs17256589	0.83[CEU][hapmap];0.82[GIH][hapmap]
rs2023532	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap]
rs3774997	0.89[ASW][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap]
rs3960787	0.83[CEU][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594957	chr4:103728010-103870091	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	esv1802717	chr4:103765156-103870091	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv2757946	chr4:103780705-104057321	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	esv2759270	chr4:103780705-104057321	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers 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	36 gene(s)	inside rSNPs	diseases
5	nsv879683	chr4:103785051-103916717	Flanking Active TSS Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	esv1849799	chr4:103787351-103881772	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2198199	TET2	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103787200-103789800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:103787600-103791000	Active TSS	K562	blood
3	chr4:103787600-103792600	Active TSS	GM12878-XiMat	blood
4	chr4:103788000-103791600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr4:103788400-103791800	Active TSS	Hela-S3	cervix
6	chr4:103788400-103792000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr4:103788600-103789800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:103788600-103791000	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr4:103788600-103791400	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr4:103788600-103791600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:103788600-103791600	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr4:103788600-103792000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:103788600-103792200	Active TSS	A549	lung
14	chr4:103788800-103789800	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr4:103788800-103790200	Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr4:103788800-103791000	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr4:103788800-103791000	Active TSS	Brain Substantia Nigra	brain
18	chr4:103788800-103791000	Active TSS	Rectal Smooth Muscle	rectum
19	chr4:103788800-103791200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr4:103788800-103791200	Active TSS	NHDF-Ad	bronchial
21	chr4:103788800-103791200	Active TSS	NHLF	lung
22	chr4:103788800-103791400	Active TSS	H9 Cell Line	embryonic stem cell
23	chr4:103788800-103791400	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr4:103788800-103791600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:103788800-103791600	Active TSS	Duodenum Mucosa	Duodenum
26	chr4:103788800-103792000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:103789000-103789800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr4:103789000-103789800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr4:103789000-103789800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr4:103789000-103789800	Active TSS	HepG2	liver
31	chr4:103789000-103790600	Active TSS	Rectal Mucosa Donor 31	rectum
32	chr4:103789000-103791000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:103789000-103791000	Active TSS	Muscle Satellite Cultured Cells	--
34	chr4:103789000-103791200	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr4:103789000-103791200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:103789000-103791200	Active TSS	Dnd41	blood
37	chr4:103789000-103791400	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr4:103789000-103791400	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr4:103789000-103791800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr4:103789000-103791800	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr4:103789000-103792000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:103789000-103792000	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr4:103789200-103789800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
44	chr4:103789200-103789800	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr4:103789200-103789800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:103789200-103790600	Active TSS	Primary T cells from cord blood	blood
47	chr4:103789200-103790600	Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr4:103789200-103790800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr4:103789200-103791000	Active TSS	Liver	Liver
50	chr4:103789200-103791000	Active TSS	Brain Anterior Caudate	brain

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