Variant report

Variant	rs6844771
Chromosome Location	chr4:99916084-99916085
allele	G/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	ZNF384	chr4:99916080-99917046	K562	blood:	n/a	n/a
2	ARID3A	chr4:99915902-99916631	K562	blood:	n/a	n/a
3	MAFF	chr4:99916014-99916603	HepG2	liver:	n/a	chr4:99916067-99916085
4	IRF1	chr4:99915826-99917076	K562	blood:	n/a	chr4:99916758-99916772 chr4:99916175-99916188
5	MYBL2	chr4:99916076-99916670	HepG2	liver:	n/a	n/a
6	CEBPB	chr4:99915863-99916148	HepG2	liver:	n/a	n/a
7	MAX	chr4:99916001-99918033	NB4	blood:	n/a	chr4:99917719-99917728
8	ZMIZ1	chr4:99915938-99917091	K562	blood:	n/a	n/a
9	CEBPB	chr4:99915822-99916462	K562	blood:	n/a	n/a
10	MAZ	chr4:99915872-99917807	IMR90	lung:	n/a	chr4:99917719-99917728
11	RAD21	chr4:99915896-99918353	SK-N-SH	brain:	n/a	chr4:99916784-99916798 chr4:99917165-99917184 chr4:99916748-99916762 chr4:99917359-99917373 chr4:99917179-99917189
12	RAD21	chr4:99915926-99916961	Hela-S3	cervix:	n/a	chr4:99916784-99916798 chr4:99916748-99916762
13	CTCF	chr4:99915873-99917978	SK-N-SH	brain:	n/a	chr4:99917075-99917084 chr4:99916508-99916521 chr4:99917169-99917182 chr4:99916506-99916522
14	WRNIP1	chr4:99915908-99916534	GM12878	blood:	n/a	n/a
15	CHD2	chr4:99916052-99917044	K562	blood:	n/a	chr4:99916801-99916811
16	PML	chr4:99916046-99917615	GM12878	blood:	n/a	n/a
17	MXI1	chr4:99915716-99918226	IMR90	lung:	n/a	n/a
18	MXI1	chr4:99915800-99918217	SK-N-SH	brain:	n/a	n/a
19	ARID3A	chr4:99915823-99916653	HepG2	liver:	n/a	n/a
20	CTCF	chr4:99916045-99917226	K562	blood:	n/a	chr4:99917075-99917084 chr4:99916508-99916521 chr4:99917169-99917182 chr4:99916506-99916522
21	CBX3	chr4:99916079-99916657	K562	blood:	n/a	n/a
22	SMC3	chr4:99916064-99917064	K562	blood:	n/a	chr4:99916507-99916521 chr4:99917023-99917033
23	EP300	chr4:99916047-99917351	SK-N-SH	brain:	n/a	chr4:99917340-99917349 chr4:99917328-99917344
24	RAD21	chr4:99915980-99917229	HCT-116	colon:	n/a	chr4:99916784-99916798 chr4:99917165-99917184 chr4:99916748-99916762 chr4:99917179-99917189
25	TBP	chr4:99916050-99916560	HepG2	liver:	n/a	n/a
26	RAD21	chr4:99916082-99917081	H1-hESC	embryonic stem cell:	n/a	chr4:99916784-99916798 chr4:99916748-99916762
27	NR2F2	chr4:99915996-99916678	K562	blood:	n/a	n/a
28	SMC3	chr4:99915950-99917532	SK-N-SH	brain:	n/a	chr4:99917169-99917183 chr4:99916507-99916521 chr4:99917172-99917182 chr4:99917179-99917189 chr4:99917023-99917033
29	SIN3AK20	chr4:99916066-99916484	H1-hESC	embryonic stem cell:	n/a	n/a
30	SMC3	chr4:99915902-99916650	HepG2	liver:	n/a	chr4:99916507-99916521
31	CTCF	chr4:99916061-99917111	GM12878	blood:	n/a	chr4:99917075-99917084 chr4:99916508-99916521 chr4:99916506-99916522
32	CTCF	chr4:99915960-99916110	HBMEC	blood vessel:	n/a	n/a
33	POLR2A	chr4:99916042-99916598	PBDE	blood:	n/a	n/a
34	ZNF143	chr4:99916071-99917081	Hela-S3	cervix:	n/a	chr4:99916832-99916842
35	MAZ	chr4:99915926-99918051	K562	blood:	n/a	chr4:99917719-99917728
36	KAP1	chr4:99916022-99916584	HEK293	kidney:	n/a	n/a
37	ZNF384	chr4:99916080-99916596	GM12878	blood:	n/a	n/a
38	CTCF	chr4:99915903-99917416	A549	lung:	n/a	chr4:99917075-99917084 chr4:99916508-99916521 chr4:99917169-99917182 chr4:99916506-99916522
39	SIN3A	chr4:99915879-99918083	H1-hESC	embryonic stem cell:	n/a	chr4:99916791-99916804 chr4:99916779-99916792
40	REST	chr4:99916003-99917891	H1-neurons	neurons:	n/a	chr4:99916776-99916789 chr4:99916791-99916804 chr4:99916592-99916605 chr4:99917756-99917765 chr4:99917353-99917366 chr4:99916772-99916792 chr4:99916761-99916774
41	IRF1	chr4:99915996-99917343	K562	blood:	n/a	chr4:99916758-99916772 chr4:99916175-99916188
42	CEBPB	chr4:99915883-99916896	Hela-S3	cervix:	n/a	n/a
43	JUND	chr4:99915972-99917134	K562	blood:	n/a	n/a
44	RAD21	chr4:99916047-99917215	HCT-116	colon:	n/a	chr4:99916784-99916798 chr4:99917165-99917184 chr4:99916748-99916762 chr4:99917179-99917189
45	MAX	chr4:99916057-99917570	HCT-116	colon:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:99916055-99916105	ProgFib	skin:	n/a
2	chr4:99916055-99916105	HCPEpiC	choroid plexus:	n/a
3	chr4:99916055-99916105	HEEpiC	esophagus:	n/a
4	chr4:99916055-99916105	GM12878	blood:	n/a
5	chr4:99916055-99916105	MCF10A-Er-Src	breast:	n/a
6	chr4:99916055-99916105	HMEC	breast:	n/a
7	chr4:99916055-99916105	ovcar-3	ovarian:	n/a
8	chr4:99916055-99916105	GM12892	blood:	n/a
9	chr4:99916055-99916105	HCT-116	colon:	n/a
10	chr4:99916055-99916105	HCF	heart:	n/a
11	chr4:99916055-99916105	HRCEpiC	kidney:	n/a
12	chr4:99916055-99916105	HCM	heart:	n/a
13	chr4:99916055-99916105	HEK293	kidney:	embryo
14	chr4:99916055-99916105	SK-N-MC	brain:	n/a
15	chr4:99916055-99916105	GM19239	blood:	n/a
16	chr4:99916055-99916105	NH-A	brain:	n/a
17	chr4:99916055-99916105	SKMC	muscle:	n/a
18	chr4:99916055-99916105	H1-hESC	embryonic stem cell:	embryo
19	chr4:99916055-99916105	HNPCEpiC	eye:	n/a
20	chr4:99916055-99916105	T-47D	breast:	n/a
21	chr4:99916055-99916105	SK-N-SH_RA	brain:	n/a
22	chr4:99916055-99916105	HIPEpiC	eye:	n/a
23	chr4:99916055-99916105	PrEC	prostate:	n/a
24	chr4:99916055-99916105	HL-60	blood:	n/a
25	chr4:99916055-99916105	NHDF-neo	bronchial:	n/a
26	chr4:99916055-99916105	HAEpiC	amniotic membrane:	n/a
27	chr4:99916055-99916105	ECC-1	luminal epithelium:	n/a
28	chr4:99916055-99916105	SK-N-SH	brain:	n/a
29	chr4:99916055-99916105	SAEC	small airway:	n/a
30	chr4:99916055-99916105	Jurkat	blood:	n/a
31	chr4:99916055-99916105	HRPEpiC	eye:	n/a
32	chr4:99916055-99916105	GM12891	blood:	n/a
33	chr4:99916055-99916105	IMR90	lung:	fetal
34	chr4:99916055-99916105	LNCaP	prostate:	n/a
35	chr4:99916055-99916105	AG04450	lung:	fetal
36	chr4:99916055-99916105	HPAEpiC	pulmonary alveolar:	n/a
37	chr4:99916055-99916105	HepG2	liver:	n/a
38	chr4:99916055-99916105	HUVEC	blood vessel:	n/a
39	chr4:99916055-99916105	Hela-S3	cervix:	n/a
40	chr4:99916055-99916105	CMK	blood:	n/a
41	chr4:99916055-99916105	PFSK-1	brain:	n/a
42	chr4:99916055-99916105	NHBE	bronchial:	n/a
43	chr4:99916055-99916105	NB4	blood:	n/a
44	chr4:99916055-99916105	NT2-D1	testis:	n/a
45	chr4:99916055-99916105	MCF-7	breast:	n/a
46	chr4:99916055-99916105	GM06990	blood:	n/a
47	chr4:99916055-99916105	AoSMC	blood vessel:	n/a
48	chr4:99916055-99916105	Hepatocyte	liver:	n/a
49	chr4:99916055-99916105	PANC-1	pancreas:	n/a
50	chr4:99916055-99916105	U87	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:99810116..99812190-chr4:99915522..99918265,3	K562	blood:
2	chr4:99916028..99916613-chr4:99971612..99972143,2	MCF-7	breast:
3	chr4:99848351..99851753-chr4:99915675..99920876,6	MCF-7	breast:
4	chr4:99830941..99833130-chr4:99915425..99918294,2	K562	blood:
5	chr4:99915525..99918321-chr4:99942451..99944575,2	K562	blood:
6	chr4:99915636..99917371-chr4:100869943..100872361,4	K562	blood:
7	chr4:99859227..99861743-chr4:99914804..99916437,2	K562	blood:
8	chr4:99915265..99918330-chr4:100008518..100010769,3	K562	blood:
9	chr4:99914813..99916738-chr4:99980811..99982387,2	MCF-7	breast:
10	chr4:99913236..99916407-chr4:99949384..99951097,3	K562	blood:
11	chr4:99846410..99852563-chr4:99914756..99918771,11	MCF-7	breast:
12	chr4:99915764..99917972-chr4:100008352..100010409,2	MCF-7	breast:
13	chr4:99830466..99832441-chr4:99915754..99918294,2	K562	blood:
14	chr4:99915328..99918402-chr4:100008331..100011431,5	MCF-7	breast:
15	chr4:99842136..99852937-chr4:99913200..99922220,39	K562	blood:
16	chr4:99914937..99918533-chr4:100007922..100010203,4	K562	blood:
17	chr4:99915655..99920524-chr4:100869895..100872849,4	K562	blood:
18	chr4:99844460..99852883-chr4:99909835..99921707,41	K562	blood:

Variant related genes	Relation type
METAP1	TF binding region
MIR3684	TF binding region
MIR3684	CpG island
METAP1	CpG island
ENSG00000250496	Chromatin interaction
ENSG00000245322	Chromatin interaction
ENSG00000164024	Chromatin interaction
ENSG00000197894	Chromatin interaction
ENSG00000263923	Chromatin interaction
ENSG00000246090	Chromatin interaction
ENSG00000151247	Chromatin interaction
ENSG00000249055	Chromatin interaction
ENSG00000238449	Chromatin interaction
ENSG00000164032	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10489130	0.84[AMR][1000 genomes]
rs17028382	0.92[AMR][1000 genomes]
rs17028421	1.00[AMR][1000 genomes]
rs35933543	1.00[AMR][1000 genomes]
rs57770074	1.00[AMR][1000 genomes]
rs58521602	0.84[AMR][1000 genomes]
rs60513719	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6532777	1.00[AMR][1000 genomes]
rs6822811	1.00[AMR][1000 genomes]
rs6834982	1.00[AMR][1000 genomes]
rs72908953	1.00[AMR][1000 genomes]
rs72908961	1.00[AMR][1000 genomes]
rs72908966	1.00[AMR][1000 genomes]
rs72908968	0.84[AMR][1000 genomes]
rs72908992	1.00[AMR][1000 genomes]
rs72908996	0.85[AMR][1000 genomes]
rs7667503	0.92[AMR][1000 genomes]
rs7670154	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99914200-99916200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:99915200-99916200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:99915200-99916200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:99915400-99918600	Active TSS	HepG2	liver
5	chr4:99915600-99916200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:99915600-99916200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:99915600-99916200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:99915600-99916200	Flanking Active TSS	A549	lung
9	chr4:99915600-99916400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:99915600-99916400	Flanking Active TSS	Dnd41	blood
11	chr4:99915600-99918200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:99915600-99918400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:99915800-99916200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr4:99915800-99916200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr4:99915800-99916200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr4:99915800-99916200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:99915800-99916200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:99915800-99916200	Flanking Active TSS	Brain Angular Gyrus	brain
19	chr4:99915800-99916200	Flanking Active TSS	Fetal Kidney	kidney
20	chr4:99915800-99916200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
21	chr4:99915800-99916200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr4:99915800-99916200	Flanking Active TSS	Thymus	Thymus
23	chr4:99915800-99916200	Flanking Active TSS	K562	blood
24	chr4:99915800-99916200	Flanking Active TSS	Osteobl	bone
25	chr4:99915800-99916400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:99915800-99916400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr4:99915800-99916400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:99915800-99916400	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr4:99915800-99916400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
30	chr4:99915800-99916400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr4:99915800-99916400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr4:99915800-99916400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:99915800-99916400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr4:99915800-99916400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr4:99915800-99916400	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr4:99915800-99916400	Flanking Active TSS	Liver	Liver
37	chr4:99915800-99916400	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr4:99915800-99916400	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr4:99915800-99916400	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr4:99915800-99916400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
41	chr4:99915800-99916400	Flanking Active TSS	Rectal Smooth Muscle	rectum
42	chr4:99915800-99916400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr4:99915800-99916400	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr4:99915800-99916400	Flanking Active TSS	GM12878-XiMat	blood
45	chr4:99915800-99916400	Flanking Active TSS	Hela-S3	cervix
46	chr4:99915800-99916400	Flanking Active TSS	HMEC	breast
47	chr4:99915800-99916400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr4:99915800-99916400	Flanking Active TSS	NHEK	skin
49	chr4:99915800-99916600	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr4:99915800-99917000	Active TSS	Brain Germinal Matrix	brain

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