Variant report

Variant	rs12076039
Chromosome Location	chr1:226899086-226899087
allele	A/T
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226898679..226899853-chr1:227014945..227016440,5	MCF-7	breast:
2	chr1:226898138..226900809-chr1:226904974..226906566,2	K562	blood:
3	chr1:226896960..226898684-chr1:226898762..226901661,3	K562	blood:
4	chr1:226821585..226822333-chr1:226899009..226899902,2	K562	blood:
5	chr1:226898531..226899526-chr1:227015550..227016285,3	K562	blood:
6	chr1:226821718..226822347-chr1:226898739..226899348,3	MCF-7	breast:
7	chr1:226891257..226894098-chr1:226898810..226900553,2	K562	blood:
8	chr1:226896960..226898684-chr1:226898762..226901394,2	K562	blood:
9	chr1:226898884..226899407-chr1:227015534..227016163,2	MCF-7	breast:
10	chr1:226898289..226900742-chr1:226913150..226915138,2	K562	blood:
11	chr1:226896184..226899571-chr1:226902737..226905068,3	K562	blood:
12	chr1:226889377..226893057-chr1:226895503..226902234,11	MCF-7	breast:
13	chr1:226889403..226893513-chr1:226896039..226901883,9	MCF-7	breast:
14	chr1:226898681..226901320-chr1:227002412..227005271,2	MCF-7	breast:
15	chr1:226898990..226899508-chr1:226911625..226912178,2	K562	blood:

No data

Extended variants
information (count: 14 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12078663	1.00[YRI][hapmap]
rs4653463	0.94[YRI][hapmap];0.94[AFR][1000 genomes]
rs4653765	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs57646605	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58304151	1.00[AMR][1000 genomes]
rs60166938	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60541195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6662364	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73100921	1.00[AMR][1000 genomes]
rs73100928	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9651015	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522446	chr1:226785530-226923938	Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv997468	chr1:226858660-226975311	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv535316	chr1:226858660-226975311	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226891600-226900600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:226891600-226900600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:226891600-226910200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:226891800-226901400	Weak transcription	Fetal Kidney	kidney
5	chr1:226891800-226903000	Enhancers	Brain Cingulate Gyrus	brain
6	chr1:226891800-226924800	Weak transcription	Aorta	Aorta
7	chr1:226893400-226918800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:226894200-226899200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:226894400-226902000	Enhancers	Brain Angular Gyrus	brain
10	chr1:226894800-226902400	Weak transcription	Psoas Muscle	Psoas
11	chr1:226895400-226899200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr1:226895400-226899400	Enhancers	HMEC	breast
13	chr1:226895400-226900200	Strong transcription	Dnd41	blood
14	chr1:226895400-226900800	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr1:226895400-226900800	Enhancers	Duodenum Mucosa	Duodenum
16	chr1:226895400-226901000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:226895600-226899200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:226895600-226901600	Enhancers	Colon Smooth Muscle	Colon
19	chr1:226895800-226899400	Enhancers	Rectal Smooth Muscle	rectum
20	chr1:226895800-226901800	Enhancers	Brain Anterior Caudate	brain
21	chr1:226896000-226899200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:226896000-226899200	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr1:226896000-226901800	Enhancers	Placenta	Placenta
24	chr1:226896000-226902600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:226896000-226903400	Enhancers	Brain Hippocampus Middle	brain
26	chr1:226896200-226899200	Genic enhancers	Fetal Thymus	thymus
27	chr1:226896200-226899400	Enhancers	Primary hematopoietic stem cells	blood
28	chr1:226896200-226899400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:226896200-226899800	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr1:226896200-226901800	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr1:226896200-226909800	Weak transcription	Fetal Intestine Large	intestine
32	chr1:226896400-226900200	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr1:226896400-226900600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:226896400-226901000	Enhancers	Adipose Nuclei	Adipose
35	chr1:226896600-226900000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr1:226896600-226901400	Enhancers	Fetal Muscle Leg	muscle
37	chr1:226896600-226910600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:226896800-226899600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:226896800-226900600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:226896800-226901200	Enhancers	Left Ventricle	heart
41	chr1:226896800-226901800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr1:226897000-226899200	Enhancers	Fetal Lung	lung
43	chr1:226897000-226899600	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr1:226897000-226901600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr1:226897000-226901800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:226897000-226901800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:226897000-226910200	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr1:226897200-226899400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:226897200-226902000	Weak transcription	Fetal Intestine Small	intestine
50	chr1:226897200-226905000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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