Variant report

Variant	rs28387060
Chromosome Location	chr3:52161643-52161644
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	chr3:52069883..52072776-chr3:52161086..52163454,2	K562	blood:
2	chr3:52152953..52156587-chr3:52160054..52162389,4	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12386365	0.81[AFR][1000 genomes]
rs12495536	0.80[EUR][1000 genomes]
rs12496447	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12629791	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2334961	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2878438	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs352152	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4687607	0.85[EUR][1000 genomes]
rs4687805	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4687810	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6773704	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6777340	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6778442	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6786592	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs731684	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs735768	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs747343	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs749995	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7644325	0.80[EUR][1000 genomes]
rs893055	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9828327	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9851576	0.85[EUR][1000 genomes]
rs9874939	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
3	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
6	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
8	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52110600-52179400	Weak transcription	Brain Germinal Matrix	brain
2	chr3:52133200-52162000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:52136800-52187200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:52140400-52178200	Strong transcription	Dnd41	blood
5	chr3:52144200-52163600	Weak transcription	Aorta	Aorta
6	chr3:52146200-52162200	Weak transcription	Gastric	stomach
7	chr3:52148600-52179800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:52152200-52164400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:52155200-52180000	Weak transcription	Fetal Intestine Large	intestine
10	chr3:52155200-52187200	Weak transcription	Colonic Mucosa	Colon
11	chr3:52155400-52162000	Weak transcription	Stomach Mucosa	stomach
12	chr3:52155600-52162000	Weak transcription	NH-A	brain
13	chr3:52155800-52162200	Weak transcription	Ovary	ovary
14	chr3:52156200-52162000	Weak transcription	HUVEC	blood vessel
15	chr3:52156200-52178000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr3:52156200-52187600	Weak transcription	Primary T cells from cord blood	blood
17	chr3:52156600-52177800	Weak transcription	Fetal Brain Female	brain
18	chr3:52157200-52162000	Weak transcription	Fetal Heart	heart
19	chr3:52157200-52162200	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:52157200-52162200	Weak transcription	Left Ventricle	heart
21	chr3:52157200-52162400	Strong transcription	Fetal Thymus	thymus
22	chr3:52157200-52166400	Weak transcription	Esophagus	oesophagus
23	chr3:52157200-52171600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:52157200-52187600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr3:52157400-52162000	Weak transcription	Placenta	Placenta
26	chr3:52157400-52162200	Weak transcription	Brain Anterior Caudate	brain
27	chr3:52157400-52164200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:52157400-52178200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr3:52157400-52187200	Weak transcription	Fetal Kidney	kidney
30	chr3:52157600-52162000	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr3:52157600-52162200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr3:52157600-52162200	Weak transcription	Lung	lung
33	chr3:52157600-52162200	Weak transcription	Right Ventricle	heart
34	chr3:52157600-52162200	Weak transcription	Spleen	Spleen
35	chr3:52157600-52162400	Weak transcription	Pancreas	Pancrea
36	chr3:52157600-52162400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:52157600-52165200	Weak transcription	GM12878-XiMat	blood
38	chr3:52157600-52178600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:52157800-52162200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:52157800-52170200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:52158000-52162400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:52158200-52162400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:52158600-52162200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:52158600-52164200	Weak transcription	Fetal Muscle Leg	muscle
45	chr3:52158600-52172000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr3:52159000-52164000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:52159200-52162000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr3:52159600-52161800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:52159800-52162000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:52159800-52162000	Weak transcription	HepG2	liver

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