Variant report

Variant	rs1263338
Chromosome Location	chr4:2939018-2939019
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:249)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:249 , 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	chr4:2936416-2939933	GM18505	blood:	n/a	n/a
2	POLR2A	chr4:2936463-2940004	GM12891	blood:	n/a	n/a
3	POLR2A	chr4:2938272-2939348	GM10847	blood:	n/a	n/a
4	POLR2A	chr4:2936427-2939614	Hela-S3	cervix:	n/a	n/a
5	FOS	chr4:2938583-2939331	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr4:2935540-2939822	Hela-S3	cervix:	n/a	n/a
7	MAX	chr4:2936301-2939648	HCT-116	colon:	n/a	n/a
8	ZNF217	chr4:2938853-2939248	MCF-7	breast:	n/a	n/a
9	RELA	chr4:2937153-2939870	GM18505	blood:	n/a	n/a
10	CHD2	chr4:2937878-2939510	GM12878	blood:	n/a	n/a
11	MTA3	chr4:2936419-2940060	GM12878	blood:	n/a	n/a
12	POLR2A	chr4:2936420-2939905	K562	blood:	n/a	n/a
13	POLR2A	chr4:2936475-2940008	GM12891	blood:	n/a	n/a
14	POLR2A	chr4:2937124-2940033	K562	blood:	n/a	n/a
15	SIN3AK20	chr4:2936414-2939621	HCT-116	colon:	n/a	n/a
16	RXRA	chr4:2938805-2939336	HepG2	liver:	n/a	n/a
17	POLR2A	chr4:2937075-2939631	H1-hESC	embryonic stem cell:	n/a	n/a
18	BCLAF1	chr4:2937706-2939670	GM12878	blood:	n/a	n/a
19	EBF1	chr4:2938521-2939453	GM12878	blood:	n/a	chr4:2939154-2939165
20	BCL11A	chr4:2938483-2939312	GM12878	blood:	n/a	n/a
21	NFATC1	chr4:2936959-2939864	GM12878	blood:	n/a	n/a
22	YY1	chr4:2939004-2939227	HCT-116	colon:	n/a	n/a
23	JUND	chr4:2937092-2939655	HCT-116	colon:	n/a	n/a
24	MYBL2	chr4:2938634-2939413	HepG2	liver:	n/a	n/a
25	POLR2A	chr4:2936428-2940062	K562	blood:	n/a	n/a
26	POLR2A	chr4:2936942-2939390	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr4:2938688-2939464	SK-N-MC	brain:	n/a	n/a
28	POLR2A	chr4:2936392-2939634	HCT-116	colon:	n/a	n/a
29	POLR2A	chr4:2936273-2939674	MCF-7	breast:	n/a	n/a
30	BATF	chr4:2938406-2939380	GM12878	blood:	n/a	n/a
31	POLR2A	chr4:2938920-2939066	A549	lung:	n/a	n/a
32	ESR1	chr4:2938877-2939236	T-47D	breast:	n/a	chr4:2939037-2939052
33	POLR2A	chr4:2938268-2939626	Raji	blood:	n/a	n/a
34	STAT1	chr4:2938593-2939454	GM12878	blood:	n/a	n/a
35	MAFK	chr4:2939015-2939453	HepG2	liver:	n/a	n/a
36	POLR2A	chr4:2936425-2939503	HCT-116	colon:	n/a	n/a
37	POLR2A	chr4:2937759-2939502	K562	blood:	n/a	n/a
38	IRF4	chr4:2938488-2939713	GM12878	blood:	n/a	n/a
39	TBL1XR1	chr4:2937858-2939653	GM12878	blood:	n/a	n/a
40	POLR2A	chr4:2936447-2940060	GM12892	blood:	n/a	n/a
41	CEBPB	chr4:2938997-2939356	HepG2	liver:	n/a	n/a
42	RXRA	chr4:2938819-2939282	HepG2	liver:	n/a	n/a
43	SIN3AK20	chr4:2938940-2939363	PANC-1	pancreas:	n/a	n/a
44	RCOR1	chr4:2938866-2939463	HepG2	liver:	n/a	n/a
45	TCF12	chr4:2938958-2939259	HepG2	liver:	n/a	n/a
46	TCF7L2	chr4:2938678-2939447	PANC-1	pancreas:	n/a	n/a
47	FOS	chr4:2938567-2939365	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr4:2938378-2939244	SK-N-SH	brain:	n/a	n/a
49	BCL11A	chr4:2939003-2939300	GM12878	blood:	n/a	n/a
50	POLR2A	chr4:2938507-2939387	A549	lung:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:2756410..2759745-chr4:2935120..2939466,6	K562	blood:
2	chr4:2830493..2833231-chr4:2936573..2940194,3	MCF-7	breast:
3	chr4:2888603..2889496-chr4:2938489..2939073,2	MCF-7	breast:
4	chr4:2903718..2915473-chr4:2930612..2941584,27	MCF-7	breast:
5	chr4:2793408..2795261-chr4:2937928..2940807,2	MCF-7	breast:
6	chr4:2795447..2803617-chr4:2934606..2939244,18	MCF-7	breast:
7	chr4:2818590..2823604-chr4:2934968..2940177,8	MCF-7	breast:
8	chr4:2790052..2809152-chr4:2930639..2948075,83	MCF-7	breast:
9	chr4:2744637..2750348-chr4:2934999..2939149,7	MCF-7	breast:
10	chr4:2845404..2847784-chr4:2938194..2940916,3	MCF-7	breast:
11	chr4:2936565..2939326-chr4:2970679..2973500,2	K562	blood:
12	chr4:2842030..2853279-chr4:2934021..2940851,24	MCF-7	breast:
13	chr4:2867681..2870567-chr4:2936383..2939288,2	MCF-7	breast:
14	chr4:2799331..2801814-chr4:2936733..2939693,2	K562	blood:
15	chr4:2936328..2940860-chr4:2961848..2966602,8	K562	blood:
16	chr4:2753882..2759883-chr4:2932429..2941474,15	MCF-7	breast:
17	chr4:2906552..2911481-chr4:2934891..2942965,11	MCF-7	breast:
18	chr18:3447926..3450158-chr4:2936583..2939331,2	MCF-7	breast:
19	chr12:104680883..104682793-chr4:2937932..2939461,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADD1-1	chr4:2938993-2939571	ENSG00000249673
2	lnc-ADD1-1	chr4:2937273-2939869	ENSG00000249673
3	lnc-ADD1-1	chr4:2937278-2939869	NR_015453
4	lnc-ADD1-1	chr4:2938884-2939571	NONHSAT094833

No data

Variant related genes	Relation type
MFSD10	TF binding region
NOP14-AS1	TF binding region
ENSG00000125388	Chromatin interaction
ENSG00000087266	Chromatin interaction
ENSG00000177426	Chromatin interaction
ENSG00000087269	Chromatin interaction
ENSG00000198431	Chromatin interaction
ENSG00000087274	Chromatin interaction
ENSG00000168884	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1012365	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1263339	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1263341	0.82[ASN][1000 genomes]
rs1263342	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1263343	0.82[ASN][1000 genomes]
rs1263344	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1263345	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1263347	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1263349	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12642795	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1419045	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16843523	0.81[ASN][1000 genomes]
rs2051560	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2071695	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2097081	0.83[ASN][1000 genomes]
rs2185885	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2237004	0.85[ASN][1000 genomes]
rs2239728	0.92[ASN][1000 genomes]
rs2282772	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2282773	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2282774	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2285084	0.92[ASN][1000 genomes]
rs2301374	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2798287	0.85[ASN][1000 genomes]
rs3796469	0.83[ASN][1000 genomes]
rs4690001	0.80[ASN][1000 genomes]
rs4690065	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4961	0.91[ASN][1000 genomes]
rs4963	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4964	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs73082333	0.82[ASN][1000 genomes]
rs73189458	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs762847	0.80[ASN][1000 genomes]
rs7664801	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription 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	52 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2936600-2939600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr4:2937200-2939600	Flanking Active TSS	HMEC	breast
3	chr4:2937200-2939800	Transcr. at gene 5' and 3'	NHEK	skin
4	chr4:2937400-2939400	Weak transcription	Ovary	ovary
5	chr4:2937600-2939200	Enhancers	Liver	Liver
6	chr4:2937600-2939200	Enhancers	Fetal Heart	heart
7	chr4:2937600-2939200	Enhancers	Fetal Thymus	thymus
8	chr4:2937600-2939200	Genic enhancers	Stomach Smooth Muscle	stomach
9	chr4:2937600-2939200	Flanking Active TSS	GM12878-XiMat	blood
10	chr4:2937600-2939600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr4:2937600-2939600	Enhancers	Stomach Mucosa	stomach
12	chr4:2937800-2939200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:2937800-2939200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:2937800-2939200	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr4:2937800-2939400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:2937800-2939400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
17	chr4:2937800-2939400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:2937800-2939400	Genic enhancers	Fetal Muscle Trunk	muscle
19	chr4:2937800-2939400	Genic enhancers	Fetal Muscle Leg	muscle
20	chr4:2937800-2939400	Enhancers	Psoas Muscle	Psoas
21	chr4:2937800-2939400	Genic enhancers	NHLF	lung
22	chr4:2937800-2939600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:2937800-2939600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr4:2937800-2939600	Enhancers	NHDF-Ad	bronchial
25	chr4:2937800-2939800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr4:2937800-2940000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:2937800-2941800	Weak transcription	Small Intestine	intestine
28	chr4:2937800-2942400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr4:2937800-2945800	Weak transcription	Fetal Kidney	kidney
30	chr4:2938000-2939200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:2938000-2939200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr4:2938000-2939200	Genic enhancers	Right Ventricle	heart
33	chr4:2938000-2939200	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr4:2938000-2939400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:2938000-2939400	Genic enhancers	Brain Hippocampus Middle	brain
36	chr4:2938000-2939400	Genic enhancers	Duodenum Mucosa	Duodenum
37	chr4:2938000-2939400	Weak transcription	HUVEC	blood vessel
38	chr4:2938000-2939600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:2938000-2939600	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr4:2938000-2939600	Weak transcription	Fetal Brain Male	brain
41	chr4:2938000-2939800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr4:2938000-2939800	Genic enhancers	Brain Germinal Matrix	brain
43	chr4:2938000-2940200	Weak transcription	Primary B cells from cord blood	blood
44	chr4:2938000-2940200	Weak transcription	Aorta	Aorta
45	chr4:2938000-2940400	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr4:2938000-2940600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr4:2938000-2945400	Genic enhancers	Primary T cells fromperipheralblood	blood
48	chr4:2938000-2960400	Weak transcription	Right Atrium	heart
49	chr4:2938200-2939400	Genic enhancers	Esophagus	oesophagus
50	chr4:2938200-2939600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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