Variant report

Variant	rs3923384
Chromosome Location	chr2:189905397-189905398
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:189896472..189898491-chr2:189903751..189905640,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10165260	1.00[CEU][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10166301	1.00[CEU][hapmap]
rs10176287	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176565	0.92[ASN][1000 genomes]
rs10194618	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11885919	0.94[ASN][1000 genomes]
rs11893117	0.94[ASN][1000 genomes]
rs11898277	0.94[ASN][1000 genomes]
rs12617111	0.94[ASN][1000 genomes]
rs13401146	0.94[ASN][1000 genomes]
rs2229495	1.00[CEU][hapmap]
rs28486035	0.92[ASN][1000 genomes]
rs28758810	0.92[ASN][1000 genomes]
rs4128538	1.00[CEU][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4128539	1.00[CEU][hapmap]
rs4666770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4667262	1.00[CEU][hapmap]
rs6434308	0.94[ASN][1000 genomes]
rs6434309	0.93[ASN][1000 genomes]
rs6434312	1.00[CEU][hapmap]
rs6434322	1.00[CEU][hapmap];0.87[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6717231	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6750027	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6760780	0.92[ASN][1000 genomes]
rs7420715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7422106	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7422861	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7422977	0.94[ASN][1000 genomes]
rs7423494	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7424947	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7558610	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7562299	0.91[CHB][hapmap]
rs7565451	0.94[ASN][1000 genomes]
rs7573709	0.94[ASN][1000 genomes]
rs7576472	0.94[ASN][1000 genomes]
rs7576474	0.94[ASN][1000 genomes]
rs7587776	0.91[ASN][1000 genomes]
rs7591905	0.92[ASN][1000 genomes]
rs7592230	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7592439	1.00[CEU][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189888000-189917400	Weak transcription	Ovary	ovary
2	chr2:189889800-189931000	Weak transcription	Esophagus	oesophagus
3	chr2:189891600-189913600	Weak transcription	Fetal Kidney	kidney
4	chr2:189893200-189932600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:189893600-189916200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:189894000-189913800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:189894600-189932800	Weak transcription	Right Ventricle	heart
8	chr2:189895200-189909000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:189895200-189940800	Strong transcription	HSMM	muscle
10	chr2:189895600-189965200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:189896000-189907400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:189896200-189962400	Weak transcription	Left Ventricle	heart
13	chr2:189896400-189922600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:189896600-189910600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:189896800-189932800	Weak transcription	Pancreas	Pancrea
16	chr2:189897000-189911000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:189897000-189949000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:189897200-189934400	Weak transcription	Gastric	stomach
19	chr2:189897400-189905800	Weak transcription	Brain Anterior Caudate	brain
20	chr2:189897400-189917400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:189897400-189932400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:189897600-189934000	Weak transcription	Lung	lung
23	chr2:189898400-189938200	Weak transcription	HMEC	breast
24	chr2:189899000-189916000	Weak transcription	Aorta	Aorta
25	chr2:189899000-189919000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:189899000-189925000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:189899000-189939200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:189900800-189964400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr2:189901000-189914200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:189901000-189919000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:189901200-189947400	Weak transcription	Fetal Brain Male	brain
32	chr2:189901400-189909000	Strong transcription	HSMMtube	muscle
33	chr2:189901600-189907200	Strong transcription	Adipose Nuclei	Adipose
34	chr2:189901600-189908000	Strong transcription	Fetal Muscle Trunk	muscle
35	chr2:189901600-189911000	Strong transcription	A549	lung
36	chr2:189902000-189910600	Strong transcription	Stomach Smooth Muscle	stomach
37	chr2:189902400-189921600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:189902600-189906400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:189902600-189911200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:189902600-189914600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:189902600-189937000	Strong transcription	NH-A	brain
42	chr2:189902800-189905400	Strong transcription	Fetal Stomach	stomach
43	chr2:189902800-189907600	Strong transcription	Fetal Intestine Large	intestine
44	chr2:189902800-189908000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:189902800-189908000	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr2:189902800-189908200	Strong transcription	Fetal Muscle Leg	muscle
47	chr2:189902800-189914400	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr2:189902800-189914800	Strong transcription	Osteobl	bone
49	chr2:189903000-189905600	Weak transcription	HUVEC	blood vessel
50	chr2:189903000-189906400	Strong transcription	Duodenum Smooth Muscle	Duodenum

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