Variant report

Variant	rs12045515
Chromosome Location	chr1:227924743-227924744
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	POLR2A	chr1:227924447-227924977	MCF10A-Er-Src	breast:	n/a	n/a
2	NFIC	chr1:227924361-227925057	ECC-1	luminal epithelium:	n/a	n/a
3	ZNF263	chr1:227924525-227925651	HEK293-T-REx	kidney:	n/a	chr1:227925421-227925442 chr1:227925381-227925390
4	POLR2A	chr1:227924617-227924905	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227922958..227924817-chr1:228133058..228135872,2	MCF-7	breast:
2	chr1:227923000..227925656-chr1:228268639..228271303,2	MCF-7	breast:

Variant related genes	Relation type
JMJD4	TF binding region
ENSG00000143761	Chromatin interaction
ENSG00000143816	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12118505	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs12141887	1.00[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227923400-227925000	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr1:227923600-227925200	Flanking Active TSS	Dnd41	blood
3	chr1:227923800-227935600	Weak transcription	Aorta	Aorta
4	chr1:227924000-227924800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:227924000-227924800	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr1:227924000-227924800	Enhancers	Muscle Satellite Cultured Cells	--
7	chr1:227924000-227924800	Enhancers	Brain Substantia Nigra	brain
8	chr1:227924000-227924800	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr1:227924000-227925000	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr1:227924000-227925000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:227924000-227925000	Enhancers	Liver	Liver
12	chr1:227924000-227925000	Enhancers	Colon Smooth Muscle	Colon
13	chr1:227924000-227925000	Enhancers	Fetal Heart	heart
14	chr1:227924000-227925000	Enhancers	Lung	lung
15	chr1:227924000-227925000	Enhancers	Right Ventricle	heart
16	chr1:227924000-227925200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:227924000-227925200	Enhancers	Fetal Stomach	stomach
18	chr1:227924000-227925200	Enhancers	Psoas Muscle	Psoas
19	chr1:227924000-227925200	Weak transcription	Small Intestine	intestine
20	chr1:227924000-227925400	Enhancers	Primary T cells fromperipheralblood	blood
21	chr1:227924000-227925400	Enhancers	Left Ventricle	heart
22	chr1:227924000-227925400	Enhancers	Pancreas	Pancrea
23	chr1:227924000-227925600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:227924000-227928200	Weak transcription	Right Atrium	heart
25	chr1:227924000-227932000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:227924000-227935400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:227924000-227935600	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr1:227924000-227936400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:227924200-227924800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:227924200-227924800	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr1:227924200-227924800	Enhancers	Brain Hippocampus Middle	brain
32	chr1:227924200-227924800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr1:227924200-227924800	Enhancers	Fetal Intestine Small	intestine
34	chr1:227924200-227924800	Enhancers	Thymus	Thymus
35	chr1:227924200-227925000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:227924200-227925000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr1:227924200-227925000	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr1:227924200-227925000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:227924200-227925000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:227924200-227925000	Enhancers	Brain Anterior Caudate	brain
41	chr1:227924200-227925000	Enhancers	Brain Cingulate Gyrus	brain
42	chr1:227924200-227925000	Enhancers	Fetal Brain Male	brain
43	chr1:227924200-227925000	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr1:227924200-227925000	Enhancers	K562	blood
45	chr1:227924200-227925000	Enhancers	NHLF	lung
46	chr1:227924200-227925200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:227924200-227925200	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr1:227924200-227925200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:227924200-227925200	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr1:227924200-227925200	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links