Variant report

Variant	rs13061
Chromosome Location	chr4:2939616-2939617
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:107)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:107 , 50 per page) page: 1 2 3

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	chr4:2935540-2939822	Hela-S3	cervix:	n/a	n/a
4	MAX	chr4:2936301-2939648	HCT-116	colon:	n/a	n/a
5	RELA	chr4:2937153-2939870	GM18505	blood:	n/a	n/a
6	MTA3	chr4:2936419-2940060	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:2936420-2939905	K562	blood:	n/a	n/a
8	POLR2A	chr4:2936475-2940008	GM12891	blood:	n/a	n/a
9	POLR2A	chr4:2937124-2940033	K562	blood:	n/a	n/a
10	SIN3AK20	chr4:2936414-2939621	HCT-116	colon:	n/a	n/a
11	POLR2A	chr4:2937075-2939631	H1-hESC	embryonic stem cell:	n/a	n/a
12	BCLAF1	chr4:2937706-2939670	GM12878	blood:	n/a	n/a
13	NFATC1	chr4:2936959-2939864	GM12878	blood:	n/a	n/a
14	JUND	chr4:2937092-2939655	HCT-116	colon:	n/a	n/a
15	POLR2A	chr4:2936428-2940062	K562	blood:	n/a	n/a
16	POLR2A	chr4:2936392-2939634	HCT-116	colon:	n/a	n/a
17	POLR2A	chr4:2936273-2939674	MCF-7	breast:	n/a	n/a
18	POLR2A	chr4:2938268-2939626	Raji	blood:	n/a	n/a
19	IRF4	chr4:2938488-2939713	GM12878	blood:	n/a	n/a
20	TBL1XR1	chr4:2937858-2939653	GM12878	blood:	n/a	n/a
21	POLR2A	chr4:2936447-2940060	GM12892	blood:	n/a	n/a
22	MAZ	chr4:2939608-2939736	GM12878	blood:	n/a	n/a
23	IKZF1	chr4:2937926-2939864	GM12878	blood:	n/a	n/a
24	POLR2A	chr4:2936416-2940081	GM12878	blood:	n/a	n/a
25	MYC	chr4:2937183-2939811	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr4:2937058-2939858	K562	blood:	n/a	n/a
27	POLR2A	chr4:2936414-2940014	GM12878	blood:	n/a	n/a
28	POLR2A	chr4:2936327-2940084	HL-60	blood:	n/a	n/a
29	POLR2A	chr4:2937183-2939836	PANC-1	pancreas:	n/a	n/a
30	WRNIP1	chr4:2938974-2939664	GM12878	blood:	n/a	n/a
31	ATF2	chr4:2937210-2939919	GM12878	blood:	n/a	n/a
32	POLR2A	chr4:2936412-2939961	GM19193	blood:	n/a	n/a
33	SP1	chr4:2938891-2939653	GM12878	blood:	n/a	n/a
34	RUNX3	chr4:2936401-2939992	GM12878	blood:	n/a	n/a
35	POLR2A	chr4:2936437-2945444	GM12892	blood:	n/a	n/a
36	STAT5A	chr4:2937180-2939913	GM12878	blood:	n/a	n/a
37	POLR2A	chr4:2936441-2940421	GM12892	blood:	n/a	n/a
38	RELA	chr4:2937113-2939893	GM12878	blood:	n/a	n/a
39	POLR2A	chr4:2936422-2940075	K562	blood:	n/a	n/a
40	RCOR1	chr4:2938370-2939791	GM12878	blood:	n/a	n/a
41	POLR2A	chr4:2936428-2939933	MCF10A-Er-Src	breast:	n/a	n/a
42	NFATC1	chr4:2936482-2940034	GM12878	blood:	n/a	n/a
43	SIN3AK20	chr4:2936456-2939662	HCT-116	colon:	n/a	n/a
44	POLR2A	chr4:2936486-2940019	GM12891	blood:	n/a	n/a
45	POLR2A	chr4:2936546-2939953	A549	lung:	n/a	n/a
46	JUND	chr4:2936426-2939677	HCT-116	colon:	n/a	n/a
47	CUX1	chr4:2938760-2939900	GM12878	blood:	n/a	n/a
48	BCLAF1	chr4:2936525-2939657	GM12878	blood:	n/a	chr4:2936597-2936606
49	FOSL2	chr4:2938518-2939687	HepG2	liver:	n/a	n/a
50	POLR2A	chr4:2936449-2940042	PANC-1	pancreas:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:2744882..2747372-chr4:2939204..2941468,2	MCF-7	breast:
2	chr4:2830493..2833231-chr4:2936573..2940194,3	MCF-7	breast:
3	chr4:2903718..2915473-chr4:2930612..2941584,27	MCF-7	breast:
4	chr4:2793408..2795261-chr4:2937928..2940807,2	MCF-7	breast:
5	chr4:2818590..2823604-chr4:2934968..2940177,8	MCF-7	breast:
6	chr4:2790052..2809152-chr4:2930639..2948075,83	MCF-7	breast:
7	chr4:2845404..2847784-chr4:2938194..2940916,3	MCF-7	breast:
8	chr4:2842030..2853279-chr4:2934021..2940851,24	MCF-7	breast:
9	chr4:2799331..2801814-chr4:2936733..2939693,2	K562	blood:
10	chr4:2936328..2940860-chr4:2961848..2966602,8	K562	blood:
11	chr4:2753882..2759883-chr4:2932429..2941474,15	MCF-7	breast:
12	chr4:2906552..2911481-chr4:2934891..2942965,11	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADD1-1	chr4:2937273-2939869	ENSG00000249673
2	lnc-ADD1-1	chr4:2937278-2939869	NR_015453

No data

Variant related genes	Relation type
MFSD10	TF binding region
ENSG00000087266	Chromatin interaction
ENSG00000168884	Chromatin interaction
ENSG00000087269	Chromatin interaction
ENSG00000087274	Chromatin interaction
ENSG00000125388	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16843596	0.83[AFR][1000 genomes]
rs16843735	1.00[EUR][1000 genomes]
rs34120252	0.83[AFR][1000 genomes]
rs34241425	0.83[AFR][1000 genomes]
rs34550139	0.83[AFR][1000 genomes]
rs34743278	0.83[AFR][1000 genomes]
rs34945392	0.83[AFR][1000 genomes]
rs35445752	0.83[AFR][1000 genomes]
rs57155428	0.83[AFR][1000 genomes]
rs57557041	0.83[AFR][1000 genomes]
rs57643304	1.00[EUR][1000 genomes]
rs58059873	0.83[AFR][1000 genomes]
rs58196520	0.83[AFR][1000 genomes]
rs58731679	0.83[AFR][1000 genomes]
rs59539429	1.00[EUR][1000 genomes]
rs61117606	0.83[AFR][1000 genomes]
rs61339714	0.83[AFR][1000 genomes]
rs61414862	1.00[EUR][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	chr4:2937200-2939800	Transcr. at gene 5' and 3'	NHEK	skin
2	chr4:2937800-2939800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr4:2937800-2940000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr4:2937800-2941800	Weak transcription	Small Intestine	intestine
5	chr4:2937800-2942400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr4:2937800-2945800	Weak transcription	Fetal Kidney	kidney
7	chr4:2938000-2939800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:2938000-2939800	Genic enhancers	Brain Germinal Matrix	brain
9	chr4:2938000-2940200	Weak transcription	Primary B cells from cord blood	blood
10	chr4:2938000-2940200	Weak transcription	Aorta	Aorta
11	chr4:2938000-2940400	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr4:2938000-2940600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr4:2938000-2945400	Genic enhancers	Primary T cells fromperipheralblood	blood
14	chr4:2938000-2960400	Weak transcription	Right Atrium	heart
15	chr4:2938200-2939800	Genic enhancers	Placenta	Placenta
16	chr4:2938200-2940600	Weak transcription	Colon Smooth Muscle	Colon
17	chr4:2938200-2946800	Strong transcription	Thymus	Thymus
18	chr4:2938200-2948400	Strong transcription	Fetal Intestine Small	intestine
19	chr4:2938200-2962200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:2938400-2940200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr4:2938400-2940400	Weak transcription	Brain Angular Gyrus	brain
22	chr4:2938400-2941200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr4:2938400-2944400	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:2938400-2957600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr4:2938400-2959600	Strong transcription	Brain Anterior Caudate	brain
26	chr4:2938400-2962200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr4:2938600-2940000	Genic enhancers	A549	lung
28	chr4:2938600-2943800	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr4:2938600-2949600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:2938600-2960400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:2938600-2960400	Strong transcription	Brain Cingulate Gyrus	brain
32	chr4:2938600-2961000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:2938600-2961600	Strong transcription	Primary T cells from cord blood	blood
34	chr4:2938600-2961600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr4:2938800-2940000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:2938800-2944000	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr4:2938800-2955600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:2938800-2956800	Strong transcription	Fetal Intestine Large	intestine
39	chr4:2938800-2959200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:2938800-2961000	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr4:2938800-2961000	Strong transcription	Primary hematopoietic stem cells	blood
42	chr4:2938800-2961000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:2939000-2939800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr4:2939000-2939800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
45	chr4:2939000-2940000	Genic enhancers	Primary B cells from peripheral blood	blood
46	chr4:2939000-2940000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr4:2939000-2943000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr4:2939000-2956800	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr4:2939000-2956800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr4:2939000-2957400	Strong transcription	HUES64 Cell Line	embryonic stem cell

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