Variant report

Variant	rs3798307
Chromosome Location	chr6:167363948-167363949
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:78)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:78 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr6:167362999-167364205	MCF-7	breast:	n/a	n/a
2	POLR2A	chr6:167363349-167365201	GM12878	blood:	n/a	n/a
3	RELA	chr6:167363624-167364279	GM18951	blood:	n/a	n/a
4	RELA	chr6:167363686-167364277	GM19193	blood:	n/a	n/a
5	POLR2A	chr6:167363141-167365064	GM19193	blood:	n/a	n/a
6	POLR2A	chr6:167363833-167364636	GM12892	blood:	n/a	n/a
7	MAFF	chr6:167363814-167364059	K562	blood:	n/a	chr6:167363922-167363940
8	ZNF143	chr6:167363704-167364144	GM12878	blood:	n/a	n/a
9	POLR2A	chr6:167363901-167365113	GM12891	blood:	n/a	n/a
10	FOXM1	chr6:167363550-167365213	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:167363085-167364460	HepG2	liver:	n/a	n/a
12	MAFF	chr6:167363767-167364096	HepG2	liver:	n/a	chr6:167363922-167363940
13	BCLAF1	chr6:167363682-167364306	GM12878	blood:	n/a	chr6:167363938-167363947
14	MAFK	chr6:167363760-167364140	HepG2	liver:	n/a	n/a
15	STAT1	chr6:167363843-167364209	GM12878	blood:	n/a	chr6:167363978-167363989
16	POLR2A	chr6:167363825-167364689	GM12878	blood:	n/a	n/a
17	FOXM1	chr6:167363688-167365268	GM12878	blood:	n/a	n/a
18	HEY1	chr6:167363848-167365006	HepG2	liver:	n/a	n/a
19	POLR2A	chr6:167363625-167364471	K562	blood:	n/a	n/a
20	RUNX3	chr6:167363695-167365243	GM12878	blood:	n/a	n/a
21	BATF	chr6:167363731-167364205	GM12878	blood:	n/a	n/a
22	POLR2A	chr6:167362977-167365124	GM12891	blood:	n/a	n/a
23	RUNX3	chr6:167363485-167364297	GM12878	blood:	n/a	n/a
24	IRF4	chr6:167363741-167365208	GM12878	blood:	n/a	n/a
25	MAFK	chr6:167363759-167364096	IMR90	lung:	n/a	n/a
26	MXI1	chr6:167363709-167365454	GM12878	blood:	n/a	n/a
27	SPI1	chr6:167363679-167364200	GM12891	blood:	n/a	n/a
28	POLR2A	chr6:167363089-167365108	GM12878	blood:	n/a	n/a
29	POLR2A	chr6:167363767-167365160	GM12891	blood:	n/a	n/a
30	SPI1	chr6:167363816-167364027	GM12878	blood:	n/a	n/a
31	MTA3	chr6:167363331-167364435	GM12878	blood:	n/a	n/a
32	MAX	chr6:167363115-167364183	MCF-7	breast:	n/a	n/a
33	MTA3	chr6:167362913-167365179	GM12878	blood:	n/a	n/a
34	WRNIP1	chr6:167363587-167364246	GM12878	blood:	n/a	n/a
35	RELA	chr6:167363485-167364409	GM18505	blood:	n/a	n/a
36	SPI1	chr6:167363697-167364196	GM12878	blood:	n/a	n/a
37	NFIC	chr6:167363666-167364233	GM12878	blood:	n/a	n/a
38	POLR2A	chr6:167363114-167365106	GM18505	blood:	n/a	n/a
39	SPI1	chr6:167363509-167364295	GM12878	blood:	n/a	n/a
40	BATF	chr6:167363773-167364130	GM12878	blood:	n/a	n/a
41	MAX	chr6:167363667-167365149	GM12878	blood:	n/a	n/a
42	ATF2	chr6:167363635-167364298	GM12878	blood:	n/a	n/a
43	BHLHE40	chr6:167363687-167365191	GM12878	blood:	n/a	n/a
44	POLR2A	chr6:167363528-167365186	GM12892	blood:	n/a	n/a
45	NFATC1	chr6:167363636-167364365	GM12878	blood:	n/a	n/a
46	RELA	chr6:167363514-167364199	GM19099	blood:	n/a	n/a
47	POU2F2	chr6:167363869-167364104	GM12878	blood:	n/a	chr6:167363933-167363946
48	STAT5A	chr6:167363616-167364319	GM12878	blood:	n/a	chr6:167363978-167363989
49	MAFK	chr6:167363755-167364109	HepG2	liver:	n/a	n/a
50	BHLHE40	chr6:167363679-167365192	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:167361983..167365004-chr6:167367480..167371949,7	MCF-7	breast:
2	chr6:167358096..167360750-chr6:167361902..167364646,4	K562	blood:
3	chr6:167362668..167365438-chr6:167411450..167414365,2	MCF-7	breast:
4	chr6:167353412..167356832-chr6:167362421..167365420,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000197146	TF binding region
ENSG00000213066	Chromatin interaction
ENSG00000272980	Chromatin interaction
ENSG00000197146	Chromatin interaction
ENSG00000026297	Chromatin interaction
ENSG00000227598	Chromatin interaction
ENSG00000249141	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1079145	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs162289	0.83[JPT][hapmap]
rs162291	0.83[JPT][hapmap]
rs162293	0.83[JPT][hapmap]
rs162294	0.83[JPT][hapmap]
rs162295	0.82[JPT][hapmap];0.82[MEX][hapmap]
rs162297	0.87[JPT][hapmap];0.87[MEX][hapmap]
rs2236312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777727	0.87[ASN][1000 genomes]
rs9366076	0.83[JPT][hapmap];0.87[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1019381	chr6:167090236-167558598	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv538541	chr6:167090236-167558598	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv948634	chr6:167200671-167838993	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
5	nsv482507	chr6:167282376-167474915	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv532074	chr6:167320656-167781977	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats 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	23 gene(s)	inside rSNPs	diseases
7	nsv1031039	chr6:167324021-167741439	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
8	nsv538543	chr6:167324021-167741439	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
9	nsv1026972	chr6:167335031-167671042	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
10	nsv1034359	chr6:167359643-167384714	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3798307	RNASET2	cis	Whole Blood	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167341000-167368800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr6:167341200-167368800	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:167342400-167368600	Weak transcription	Fetal Heart	heart
4	chr6:167344200-167364000	Weak transcription	Brain Angular Gyrus	brain
5	chr6:167344200-167368600	Weak transcription	Right Atrium	heart
6	chr6:167344400-167364000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:167348400-167364800	Weak transcription	Brain Substantia Nigra	brain
8	chr6:167350600-167366400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:167350600-167367600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:167352200-167368800	Weak transcription	Fetal Kidney	kidney
11	chr6:167352400-167364800	Weak transcription	Right Ventricle	heart
12	chr6:167353600-167364000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr6:167353800-167366600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:167354400-167364800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:167354600-167364800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:167354600-167368800	Weak transcription	HSMM	muscle
17	chr6:167354600-167369000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr6:167354600-167369000	Weak transcription	A549	lung
19	chr6:167356400-167366800	Strong transcription	Fetal Intestine Small	intestine
20	chr6:167357200-167364000	Weak transcription	Left Ventricle	heart
21	chr6:167359200-167365400	Strong transcription	Primary hematopoietic stem cells	blood
22	chr6:167360000-167368800	Weak transcription	Fetal Lung	lung
23	chr6:167360600-167368800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:167360600-167368800	Weak transcription	Fetal Muscle Leg	muscle
25	chr6:167360600-167369000	Weak transcription	Osteobl	bone
26	chr6:167361200-167364800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr6:167361200-167366200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr6:167361200-167369000	Weak transcription	Ovary	ovary
29	chr6:167361200-167369200	Weak transcription	Aorta	Aorta
30	chr6:167361400-167364000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr6:167361400-167364000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr6:167361800-167368600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:167361800-167369000	Weak transcription	Psoas Muscle	Psoas
34	chr6:167362200-167365800	Genic enhancers	HepG2	liver
35	chr6:167362200-167368800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr6:167362600-167365400	Enhancers	Placenta	Placenta
37	chr6:167363000-167364000	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr6:167363000-167364200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:167363000-167364400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
40	chr6:167363000-167364800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr6:167363000-167366000	Genic enhancers	Fetal Thymus	thymus
42	chr6:167363000-167368000	Genic enhancers	Primary monocytes fromperipheralblood	blood
43	chr6:167363200-167364000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr6:167363200-167364000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:167363200-167364000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr6:167363200-167364000	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr6:167363200-167364000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr6:167363200-167364000	Enhancers	Adipose Nuclei	Adipose
49	chr6:167363200-167364000	Genic enhancers	Fetal Stomach	stomach
50	chr6:167363200-167364000	Enhancers	Gastric	stomach

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