Variant report

Variant	rs28841614
Chromosome Location	chr5:52401910-52401911
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	chr5:52398859..52401960-chr5:52403484..52405544,3	K562	blood:
2	chr5:52399514..52401960-chr5:52403484..52405590,2	K562	blood:

Variant related genes	Relation type
ENSG00000164172	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10044163	0.89[AFR][1000 genomes]
rs10045657	0.89[AFR][1000 genomes]
rs10051425	0.88[EUR][1000 genomes]
rs10051483	0.88[EUR][1000 genomes]
rs10052267	0.89[AFR][1000 genomes]
rs10055919	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10058715	0.85[EUR][1000 genomes]
rs10064796	0.89[AFR][1000 genomes]
rs10065574	0.85[EUR][1000 genomes]
rs10072821	0.86[AFR][1000 genomes]
rs1042324	0.91[EUR][1000 genomes]
rs10471372	0.91[AFR][1000 genomes]
rs10471829	0.91[EUR][1000 genomes]
rs10471830	0.91[EUR][1000 genomes]
rs10471831	0.87[AFR][1000 genomes]
rs10471832	0.87[AFR][1000 genomes]
rs10513009	0.88[EUR][1000 genomes]
rs1139484	0.81[EUR][1000 genomes]
rs13356629	1.00[ASN][1000 genomes]
rs13357783	0.88[EUR][1000 genomes]
rs1445940	0.91[EUR][1000 genomes]
rs16880872	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16880873	0.91[EUR][1000 genomes]
rs16880890	0.86[AFR][1000 genomes]
rs16880892	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16880902	0.89[AFR][1000 genomes]
rs1801106	0.82[EUR][1000 genomes]
rs2052567	0.89[AFR][1000 genomes]
rs2062562	0.89[AFR][1000 genomes]
rs2193969	0.82[EUR][1000 genomes]
rs2233214	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287873	0.85[EUR][1000 genomes]
rs2303120	0.86[EUR][1000 genomes]
rs2303125	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28413530	0.89[ASN][1000 genomes]
rs28861745	0.87[AFR][1000 genomes]
rs28890193	0.89[AFR][1000 genomes]
rs2910966	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2974984	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3021373	0.81[EUR][1000 genomes]
rs3212327	0.85[EUR][1000 genomes]
rs3212429	0.89[ASN][1000 genomes]
rs3212444	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212468	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212487	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212492	0.81[EUR][1000 genomes]
rs3212497	1.00[ASN][1000 genomes]
rs3212498	0.81[EUR][1000 genomes]
rs3212503	0.81[EUR][1000 genomes]
rs3212504	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212515	1.00[ASN][1000 genomes]
rs3212526	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212528	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212529	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212536	0.83[EUR][1000 genomes]
rs3212539	0.83[EUR][1000 genomes]
rs3212543	0.83[EUR][1000 genomes]
rs3212544	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212545	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3212546	0.85[EUR][1000 genomes]
rs3212548	0.85[EUR][1000 genomes]
rs3212558	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212567	0.85[EUR][1000 genomes]
rs3212568	0.85[EUR][1000 genomes]
rs3212569	0.85[EUR][1000 genomes]
rs3212570	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212573	0.85[EUR][1000 genomes]
rs3212579	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212580	0.85[EUR][1000 genomes]
rs3212582	0.85[EUR][1000 genomes]
rs3212583	0.85[EUR][1000 genomes]
rs3212584	0.85[EUR][1000 genomes]
rs3212585	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212586	0.83[EUR][1000 genomes]
rs3212588	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212593	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212606	0.88[EUR][1000 genomes]
rs3212607	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212612	0.88[EUR][1000 genomes]
rs3212613	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212615	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212628	0.88[EUR][1000 genomes]
rs3212629	0.88[EUR][1000 genomes]
rs3212630	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3212633	0.88[EUR][1000 genomes]
rs3212634	0.88[EUR][1000 genomes]
rs3212635	0.88[EUR][1000 genomes]
rs3212643	0.88[EUR][1000 genomes]
rs3213805	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797468	0.89[AFR][1000 genomes]
rs3797469	0.89[AFR][1000 genomes]
rs3797474	0.85[EUR][1000 genomes]
rs3815755	0.85[EUR][1000 genomes]
rs3846488	0.89[AFR][1000 genomes]
rs4555727	0.89[AFR][1000 genomes]
rs7446448	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7700416	0.91[EUR][1000 genomes]
rs7737412	0.91[EUR][1000 genomes]
rs875657	0.91[EUR][1000 genomes]
rs9292008	0.88[AFR][1000 genomes]
rs9292009	0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52370400-52404600	Weak transcription	Brain Germinal Matrix	brain
2	chr5:52372400-52404400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:52378400-52405000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:52387600-52405000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:52389400-52404800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:52390200-52403800	Strong transcription	Skeletal Muscle Female	skeletal muscle
7	chr5:52390800-52403800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:52391000-52403000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr5:52391600-52403200	Weak transcription	Fetal Heart	heart
10	chr5:52392000-52404800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:52392400-52403000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr5:52392400-52403400	Strong transcription	Liver	Liver
13	chr5:52392400-52404800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:52392800-52403000	Strong transcription	Adipose Nuclei	Adipose
15	chr5:52392800-52403400	Strong transcription	Left Ventricle	heart
16	chr5:52392800-52403600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:52393000-52405000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr5:52393800-52404800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr5:52394600-52402400	Strong transcription	Primary T cells from cord blood	blood
20	chr5:52394600-52402600	Strong transcription	Fetal Thymus	thymus
21	chr5:52394800-52403600	Strong transcription	Primary B cells from cord blood	blood
22	chr5:52395400-52402200	Weak transcription	A549	lung
23	chr5:52395400-52404800	Weak transcription	Aorta	Aorta
24	chr5:52395400-52405200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr5:52395600-52403200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr5:52395600-52404400	Weak transcription	Thymus	Thymus
27	chr5:52395600-52404600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:52395600-52404800	Weak transcription	Colonic Mucosa	Colon
29	chr5:52395600-52404800	Weak transcription	Esophagus	oesophagus
30	chr5:52395600-52404800	Weak transcription	Fetal Brain Male	brain
31	chr5:52395600-52404800	Weak transcription	Pancreas	Pancrea
32	chr5:52395600-52404800	Weak transcription	Right Ventricle	heart
33	chr5:52395600-52405000	Weak transcription	Gastric	stomach
34	chr5:52395600-52405400	Weak transcription	Spleen	Spleen
35	chr5:52395800-52404600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr5:52395800-52404600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr5:52395800-52404800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr5:52395800-52405000	Weak transcription	Lung	lung
39	chr5:52395800-52405200	Weak transcription	Small Intestine	intestine
40	chr5:52396200-52404800	Weak transcription	Brain Angular Gyrus	brain
41	chr5:52396200-52404800	Weak transcription	Ovary	ovary
42	chr5:52396400-52402600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr5:52396400-52404600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr5:52396400-52404800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr5:52396600-52404400	Weak transcription	Primary hematopoietic stem cells	blood
46	chr5:52396600-52404800	Weak transcription	Brain Substantia Nigra	brain
47	chr5:52397000-52404200	Weak transcription	GM12878-XiMat	blood
48	chr5:52397200-52404400	Weak transcription	Brain Anterior Caudate	brain
49	chr5:52397400-52403200	Weak transcription	Hela-S3	cervix
50	chr5:52397400-52404400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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