Variant report

Variant	rs2077840
Chromosome Location	chr1:225963213-225963214
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:225956937..225960087-chr1:225960479..225963654,4	K562	blood:
2	chr1:225961838..225964716-chr1:226068822..226070788,2	K562	blood:
3	chr1:225960600..225963224-chr1:225967142..225968691,2	K562	blood:
4	chr1:225961965..225964037-chr1:226163126..226165079,2	K562	blood:
5	chr1:225962862..225967352-chr1:225996084..226002774,11	MCF-7	breast:
6	chr1:225959006..225964473-chr1:225964619..225968366,9	MCF-7	breast:
7	chr1:225961998..225963794-chr1:225997019..225999603,2	K562	blood:
8	chr1:225962294..225967531-chr1:225994011..226002080,11	K562	blood:

No data

Variant related genes	Relation type
ENSG00000196187	Chromatin interaction
ENSG00000143742	Chromatin interaction
ENSG00000143819	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs16845207	1.00[EUR][1000 genomes]
rs16845221	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16845230	0.85[EUR][1000 genomes]
rs16845250	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs2840964	1.00[JPT][hapmap]
rs56052403	1.00[EUR][1000 genomes]
rs74148698	0.85[ASN][1000 genomes]
rs74148699	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][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	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225952200-225964400	Weak transcription	Fetal Brain Female	brain
2	chr1:225952200-225965600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:225954800-225964400	Weak transcription	Small Intestine	intestine
4	chr1:225956800-225964600	Weak transcription	Right Ventricle	heart
5	chr1:225957000-225965000	Weak transcription	Gastric	stomach
6	chr1:225958000-225963600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:225958200-225963400	Enhancers	HSMM	muscle
8	chr1:225958600-225964800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:225959200-225964600	Weak transcription	Psoas Muscle	Psoas
10	chr1:225959200-225964800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:225959600-225964800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:225959600-225964800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:225959800-225964400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:225960000-225964600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:225960000-225964600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:225960200-225964200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:225960200-225964400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:225960200-225964800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:225960400-225963800	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr1:225960400-225964200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:225960400-225964400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:225960400-225964400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr1:225960400-225964400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:225960400-225964400	Weak transcription	Brain Substantia Nigra	brain
25	chr1:225960400-225964400	Weak transcription	Fetal Muscle Leg	muscle
26	chr1:225960400-225964400	Weak transcription	HUVEC	blood vessel
27	chr1:225960400-225964400	Weak transcription	NHDF-Ad	bronchial
28	chr1:225960400-225964600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:225960400-225965000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:225960600-225964200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr1:225960600-225964400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:225960600-225964600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:225960600-225964600	Weak transcription	Fetal Brain Male	brain
34	chr1:225960600-225964600	Weak transcription	Fetal Heart	heart
35	chr1:225960600-225964800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:225960800-225964000	Weak transcription	Fetal Intestine Large	intestine
37	chr1:225960800-225964000	Weak transcription	Fetal Thymus	thymus
38	chr1:225960800-225964200	Weak transcription	Brain Germinal Matrix	brain
39	chr1:225960800-225964200	Weak transcription	Fetal Stomach	stomach
40	chr1:225960800-225964200	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr1:225960800-225964200	Weak transcription	Thymus	Thymus
42	chr1:225960800-225964400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:225960800-225964400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:225960800-225964400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:225960800-225964400	Weak transcription	Adipose Nuclei	Adipose
46	chr1:225960800-225964400	Weak transcription	Liver	Liver
47	chr1:225960800-225964400	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:225960800-225964400	Weak transcription	Fetal Kidney	kidney
49	chr1:225960800-225964400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:225960800-225964400	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links