Variant report

Variant	rs13116185
Chromosome Location	chr4:2856687-2856688
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:2855740..2858209-chr4:2858751..2860482,2	K562	blood:
2	chr4:2855341..2858315-chr4:2935063..2937111,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SH3BP2-2	chr4:2856581-2856756	NONHSAT094815

Variant related genes	Relation type
ENSG00000109736	Chromatin interaction
ENSG00000249673	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs13103004	1.00[CEU][hapmap]
rs34036158	1.00[AMR][1000 genomes]
rs66960451	1.00[AMR][1000 genomes];0.86[EUR][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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2846600-2862400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:2846800-2857400	Weak transcription	Aorta	Aorta
3	chr4:2846800-2861800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:2846800-2861800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:2846800-2862000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:2846800-2862600	Weak transcription	Esophagus	oesophagus
7	chr4:2847200-2862200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr4:2847400-2859800	Weak transcription	A549	lung
9	chr4:2847400-2863600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:2848000-2861200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr4:2850000-2860400	Weak transcription	Fetal Brain Male	brain
12	chr4:2851000-2860000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr4:2851400-2857400	Weak transcription	Pancreas	Pancrea
14	chr4:2852000-2860200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:2852000-2865800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:2852600-2858200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr4:2853400-2859800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:2853400-2860000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:2853400-2861200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr4:2853400-2861400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr4:2854200-2857000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:2854400-2859800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:2854600-2856800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:2854600-2857000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:2854600-2857000	Strong transcription	Dnd41	blood
26	chr4:2854600-2857600	Weak transcription	Right Atrium	heart
27	chr4:2854600-2858400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:2854800-2857000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:2854800-2857200	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr4:2854800-2857400	Weak transcription	Brain Substantia Nigra	brain
31	chr4:2854800-2860200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr4:2854800-2862000	Weak transcription	NHEK	skin
33	chr4:2854800-2862800	Weak transcription	Gastric	stomach
34	chr4:2855000-2857000	Strong transcription	Fetal Brain Female	brain
35	chr4:2855000-2858200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr4:2855000-2859400	Weak transcription	NHLF	lung
37	chr4:2855000-2859600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:2855000-2860000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr4:2855000-2860000	Weak transcription	Stomach Mucosa	stomach
40	chr4:2855000-2863000	Genic enhancers	Primary B cells from peripheral blood	blood
41	chr4:2855000-2863400	Weak transcription	Brain Angular Gyrus	brain
42	chr4:2855200-2856800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr4:2855200-2857000	Genic enhancers	Duodenum Mucosa	Duodenum
44	chr4:2855200-2859400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr4:2855200-2860400	Strong transcription	Fetal Thymus	thymus
46	chr4:2855200-2862400	Genic enhancers	Primary B cells from cord blood	blood
47	chr4:2855400-2856800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr4:2855400-2856800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr4:2855400-2856800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr4:2855400-2856800	Strong transcription	Small Intestine	intestine

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