Variant report

Variant	rs2671274
Chromosome Location	chr1:226001838-226001839
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225998808..226002827-chr1:226008223..226011228,3	MCF-7	breast:
2	chr1:225962862..225967352-chr1:225996084..226002774,11	MCF-7	breast:
3	chr1:225962294..225967531-chr1:225994011..226002080,11	K562	blood:
4	chr1:226000008..226002119-chr1:226004674..226006661,2	MCF-7	breast:
5	chr1:225963814..225970754-chr1:225996230..226002908,14	MCF-7	breast:
6	chr1:225840822..225842484-chr1:226000425..226002809,2	MCF-7	breast:
7	chr1:225999526..226002981-chr1:226005681..226008708,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154380	Chromatin interaction
ENSG00000143742	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1050033	0.88[AMR][1000 genomes]
rs12031296	0.85[AMR][1000 genomes]
rs12037640	0.88[AMR][1000 genomes]
rs12045030	0.88[AMR][1000 genomes]
rs12737161	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12749689	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3820231	0.86[AMR][1000 genomes]
rs56866192	0.85[AMR][1000 genomes]
rs71646745	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71646746	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7539372	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv947519	chr1:225998770-226034631	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225998400-226007800	Enhancers	Spleen	Spleen
2	chr1:225998600-226005600	Enhancers	Stomach Mucosa	stomach
3	chr1:225999000-226002800	Enhancers	Placenta	Placenta
4	chr1:225999200-226002400	Enhancers	Esophagus	oesophagus
5	chr1:225999200-226002400	Enhancers	Fetal Intestine Large	intestine
6	chr1:225999200-226004800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:225999200-226006400	Enhancers	Lung	lung
8	chr1:225999200-226006600	Enhancers	Psoas Muscle	Psoas
9	chr1:225999400-226004600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:225999400-226004800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:225999400-226006600	Enhancers	Right Ventricle	heart
12	chr1:225999400-226007800	Enhancers	Left Ventricle	heart
13	chr1:225999600-226002400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:225999600-226003600	Enhancers	Brain Angular Gyrus	brain
15	chr1:225999600-226003800	Enhancers	Pancreas	Pancrea
16	chr1:225999600-226005200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:225999600-226006400	Enhancers	Brain Cingulate Gyrus	brain
18	chr1:225999800-226002800	Genic enhancers	Fetal Intestine Small	intestine
19	chr1:225999800-226004400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:225999800-226006400	Enhancers	Brain Hippocampus Middle	brain
21	chr1:226000000-226003400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:226000000-226003400	Genic enhancers	Fetal Muscle Trunk	muscle
23	chr1:226000000-226005400	Weak transcription	Thymus	Thymus
24	chr1:226000000-226006600	Enhancers	Brain Substantia Nigra	brain
25	chr1:226000000-226019400	Weak transcription	Fetal Brain Female	brain
26	chr1:226000200-226002600	Genic enhancers	Fetal Muscle Leg	muscle
27	chr1:226000200-226006400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:226000400-226002000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:226000400-226002800	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr1:226000400-226002800	Enhancers	Small Intestine	intestine
31	chr1:226000400-226004400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:226000400-226007400	Enhancers	Brain Anterior Caudate	brain
33	chr1:226000400-226015800	Enhancers	Ovary	ovary
34	chr1:226000600-226002000	Flanking Active TSS	A549	lung
35	chr1:226000600-226002600	Enhancers	NHLF	lung
36	chr1:226000600-226004400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:226000800-226002000	Enhancers	Fetal Stomach	stomach
38	chr1:226000800-226002000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr1:226000800-226002600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr1:226001000-226002000	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr1:226001000-226002600	Enhancers	Gastric	stomach
42	chr1:226001000-226004000	Weak transcription	Fetal Brain Male	brain
43	chr1:226001000-226004400	Weak transcription	Fetal Heart	heart
44	chr1:226001400-226003600	Enhancers	Right Atrium	heart
45	chr1:226001400-226004200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:226001400-226005000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr1:226001400-226005200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:226001400-226005400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:226001600-226002000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:226001600-226002000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links