Variant report

Variant	rs16843459
Chromosome Location	chr4:2851252-2851253
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	RAD21	chr4:2851124-2851319	HepG2	liver:	n/a	n/a
2	HNF4G	chr4:2851101-2851317	HepG2	liver:	n/a	chr4:2851175-2851190 chr4:2851176-2851189 chr4:2851175-2851190 chr4:2851176-2851188 chr4:2851173-2851188 chr4:2851175-2851190
3	FOXA2	chr4:2851157-2851372	HepG2	liver:	n/a	n/a
4	RAD21	chr4:2850856-2851959	SK-N-SH	brain:	n/a	n/a
5	HNF4A	chr4:2851111-2851299	HepG2	liver:	n/a	chr4:2851175-2851190 chr4:2851174-2851189 chr4:2851176-2851189 chr4:2851175-2851190 chr4:2851176-2851188 chr4:2851175-2851190

No.	Distal block	Cell Line	Cell type
1	chr4:2843889..2847586-chr4:2849028..2855037,6	K562	blood:
2	chr4:2843310..2847623-chr4:2847879..2851865,7	K562	blood:
3	chr4:2842030..2853279-chr4:2934021..2940851,24	MCF-7	breast:
4	chr4:2850138..2853377-chr4:2934213..2937642,3	MCF-7	breast:

Variant related genes	Relation type
ADD1	TF binding region
ENSG00000249673	Chromatin interaction
ENSG00000087274	Chromatin interaction
ENSG00000109736	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs16843490	1.00[AMR][1000 genomes]
rs16843682	1.00[AMR][1000 genomes]
rs35304823	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35983864	1.00[AMR][1000 genomes]
rs55676948	1.00[AMR][1000 genomes]
rs56315133	1.00[AMR][1000 genomes]
rs57551202	1.00[AMR][1000 genomes]
rs57960709	1.00[AMR][1000 genomes]
rs58279895	1.00[AMR][1000 genomes]
rs60514033	1.00[AMR][1000 genomes]
rs61652297	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61747144	1.00[AMR][1000 genomes]
rs6830234	1.00[AMR][1000 genomes]
rs73792109	1.00[AMR][1000 genomes]
rs73792110	1.00[AMR][1000 genomes]
rs73792112	1.00[AMR][1000 genomes]
rs73792115	1.00[AMR][1000 genomes]
rs73792116	1.00[AMR][1000 genomes]
rs73794816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73794824	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73794825	1.00[AMR][1000 genomes]
rs73794827	1.00[AMR][1000 genomes]
rs7657843	1.00[AMR][1000 genomes]
rs7676937	1.00[AMR][1000 genomes]
rs7699427	1.00[AMR][1000 genomes]

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	nsv878444	chr4:2689449-2861090	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv878450	chr4:2760222-2861090	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv593435	chr4:2770772-2881256	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv878451	chr4:2785556-2856687	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1010533	chr4:2792848-2873441	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv521858	chr4:2846799-2881256	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv526059	chr4:2850142-2861090	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv524060	chr4:2850142-2881256	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2846600-2854400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:2846600-2862400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:2846800-2854200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:2846800-2855400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr4:2846800-2855400	Weak transcription	Placenta	Placenta
6	chr4:2846800-2855600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr4:2846800-2857400	Weak transcription	Aorta	Aorta
8	chr4:2846800-2861800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:2846800-2861800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr4:2846800-2862000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:2846800-2862600	Weak transcription	Esophagus	oesophagus
12	chr4:2847200-2852000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr4:2847200-2853600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr4:2847200-2862200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr4:2847400-2852800	Weak transcription	Fetal Thymus	thymus
16	chr4:2847400-2854400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr4:2847400-2854400	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr4:2847400-2859800	Weak transcription	A549	lung
19	chr4:2847400-2863600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr4:2847800-2852000	Enhancers	K562	blood
21	chr4:2847800-2852600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:2847800-2854200	Enhancers	Primary B cells from peripheral blood	blood
23	chr4:2847800-2854200	Weak transcription	NH-A	brain
24	chr4:2847800-2854200	Weak transcription	Osteobl	bone
25	chr4:2847800-2854600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:2847800-2854800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr4:2847800-2855400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr4:2847800-2856200	Weak transcription	HMEC	breast
29	chr4:2848000-2851400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:2848000-2853000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr4:2848000-2854200	Weak transcription	HUVEC	blood vessel
32	chr4:2848000-2854400	Weak transcription	NHEK	skin
33	chr4:2848000-2855400	Weak transcription	Fetal Stomach	stomach
34	chr4:2848000-2861200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr4:2848200-2854200	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr4:2848200-2854200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr4:2848400-2851400	Enhancers	Primary T cells fromperipheralblood	blood
38	chr4:2848400-2851400	Enhancers	Left Ventricle	heart
39	chr4:2848400-2855400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr4:2848600-2851800	Enhancers	Right Ventricle	heart
41	chr4:2848800-2852000	Enhancers	Liver	Liver
42	chr4:2849000-2851800	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr4:2849000-2852000	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr4:2849000-2853600	Enhancers	HepG2	liver
45	chr4:2849200-2851400	Enhancers	Duodenum Mucosa	Duodenum
46	chr4:2849200-2851600	Enhancers	Fetal Muscle Leg	muscle
47	chr4:2849200-2851800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr4:2849200-2852000	Enhancers	Rectal Smooth Muscle	rectum
49	chr4:2849200-2852800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr4:2849200-2854200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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