Variant report

Variant	rs12989840
Chromosome Location	chr2:153329601-153329602
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:153328146..153330092-chr2:153417447..153419357,2	K562	blood:
2	chr2:153326388..153330903-chr2:153339849..153343861,4	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12104452	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12987348	0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs12991474	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12993239	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12999189	1.00[EUR][1000 genomes]
rs13011850	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13018434	1.00[EUR][1000 genomes]
rs13021931	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13023943	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs13027160	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13027356	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13029667	1.00[EUR][1000 genomes]
rs13034458	1.00[EUR][1000 genomes]
rs34300140	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34332337	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34416306	1.00[EUR][1000 genomes]
rs34457645	1.00[EUR][1000 genomes]
rs34504342	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34722196	1.00[EUR][1000 genomes]
rs35199259	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35472114	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35804350	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs36108117	1.00[EUR][1000 genomes]
rs6434046	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6731516	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6745613	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs71417227	1.00[EUR][1000 genomes]
rs71417229	1.00[EUR][1000 genomes]
rs73016010	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7562904	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv875291	chr2:153251742-153339823	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	esv2754362	chr2:153297577-153366129	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv875292	chr2:153308471-153357383	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv2830258	chr2:153318339-153349165	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153320800-153331600	Enhancers	Hela-S3	cervix
2	chr2:153324400-153331000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:153324600-153330800	Enhancers	Fetal Intestine Small	intestine
4	chr2:153324800-153340000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:153325800-153330000	Enhancers	Small Intestine	intestine
6	chr2:153326000-153329800	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr2:153326000-153330000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:153326000-153330800	Enhancers	Stomach Mucosa	stomach
9	chr2:153326000-153331600	Enhancers	Brain Cingulate Gyrus	brain
10	chr2:153326200-153330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:153326200-153330600	Weak transcription	Lung	lung
12	chr2:153326200-153332600	Weak transcription	Adipose Nuclei	Adipose
13	chr2:153326200-153333000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:153326200-153334200	Enhancers	Brain Anterior Caudate	brain
15	chr2:153326200-153339200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:153326200-153345800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:153326800-153330200	Enhancers	Rectal Smooth Muscle	rectum
18	chr2:153327200-153330800	Enhancers	Fetal Intestine Large	intestine
19	chr2:153327200-153330800	Enhancers	Fetal Lung	lung
20	chr2:153327400-153331400	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr2:153327600-153330800	Enhancers	Liver	Liver
22	chr2:153327600-153330800	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr2:153328000-153329800	Enhancers	Left Ventricle	heart
24	chr2:153328000-153333200	Enhancers	Psoas Muscle	Psoas
25	chr2:153328200-153332400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:153328400-153332600	Weak transcription	Aorta	Aorta
27	chr2:153328600-153330200	Enhancers	Placenta	Placenta
28	chr2:153328600-153330600	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr2:153328600-153332400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:153328600-153334600	Enhancers	Brain Substantia Nigra	brain
31	chr2:153329000-153329800	Enhancers	NHEK	skin
32	chr2:153329000-153330400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:153329000-153330400	Flanking Active TSS	A549	lung
34	chr2:153329000-153330600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:153329000-153330800	Enhancers	Pancreas	Pancrea
36	chr2:153329000-153337200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:153329000-153337800	Weak transcription	Fetal Stomach	stomach
38	chr2:153329200-153330000	Weak transcription	Fetal Kidney	kidney
39	chr2:153329200-153331800	Enhancers	Brain Hippocampus Middle	brain
40	chr2:153329200-153340000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:153329400-153330600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr2:153329400-153337600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr2:153329400-153338000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr2:153329600-153330200	Enhancers	HepG2	liver
45	chr2:153329600-153332400	Weak transcription	Brain Angular Gyrus	brain
46	chr2:153329600-153333600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:153329600-153337200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr2:153329600-153338200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr2:153329600-153338200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr2:153329600-153340000	Weak transcription	Ovary	ovary

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