Variant report

Variant	rs28583552
Chromosome Location	chr4:3125050-3125051
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3122978..3125681-chr4:3127694..3131057,3	K562	blood:
2	chr4:3112929..3115298-chr4:3124048..3126368,4	MCF-7	breast:
3	chr4:3123809..3125858-chr4:3463615..3466530,2	MCF-7	breast:
4	chr4:3112475..3121644-chr4:3122211..3126506,10	MCF-7	breast:
5	chr4:3119274..3122610-chr4:3124266..3127646,4	K562	blood:

Variant related genes	Relation type
ENSG00000197386	Chromatin interaction
ENSG00000175920	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10000252	0.83[EUR][1000 genomes]
rs10002065	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10006129	0.81[EUR][1000 genomes]
rs10006977	0.84[EUR][1000 genomes]
rs10009229	0.97[EUR][1000 genomes]
rs10009935	0.81[EUR][1000 genomes]
rs10011127	0.97[EUR][1000 genomes]
rs10014333	0.84[EUR][1000 genomes]
rs10016755	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10030079	0.83[EUR][1000 genomes]
rs10034313	0.90[EUR][1000 genomes]
rs10222986	0.84[EUR][1000 genomes]
rs1419036	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16843857	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16843866	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16843869	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16843871	0.98[AFR][1000 genomes]
rs28387056	0.90[EUR][1000 genomes]
rs28393280	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28394705	0.81[EUR][1000 genomes]
rs28485764	0.81[EUR][1000 genomes]
rs28580164	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28584232	0.81[EUR][1000 genomes]
rs28629394	0.81[EUR][1000 genomes]
rs28634516	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28652828	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28660254	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28670335	0.90[EUR][1000 genomes]
rs28696693	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28714390	0.81[EUR][1000 genomes]
rs28718346	0.84[EUR][1000 genomes]
rs28755900	0.87[EUR][1000 genomes]
rs3025836	0.90[EUR][1000 genomes]
rs363138	0.90[EUR][1000 genomes]
rs4346595	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56021098	0.98[AFR][1000 genomes]
rs56134819	0.81[AFR][1000 genomes]
rs56148664	0.93[AFR][1000 genomes]
rs57792935	0.93[AFR][1000 genomes]
rs57875258	0.92[AFR][1000 genomes]
rs6830019	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6835897	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6836289	0.93[AFR][1000 genomes]
rs7436457	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7664480	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7693317	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9994689	0.90[EUR][1000 genomes]
rs9995782	0.90[EUR][1000 genomes]
rs9996075	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3088200-3164200	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr4:3097200-3143400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:3097200-3162200	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr4:3097400-3163800	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr4:3098000-3162600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:3100000-3159400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:3106400-3145000	Strong transcription	Dnd41	blood
8	chr4:3106800-3125200	Strong transcription	Primary B cells from cord blood	blood
9	chr4:3108600-3125800	Strong transcription	Primary B cells from peripheral blood	blood
10	chr4:3108600-3136600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:3108600-3163000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr4:3108800-3164600	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr4:3109200-3142600	Strong transcription	GM12878-XiMat	blood
14	chr4:3109400-3130400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:3111600-3125400	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr4:3114600-3292400	Weak transcription	Right Atrium	heart
17	chr4:3114800-3162800	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr4:3115800-3143400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr4:3115800-3161600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:3115800-3162800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr4:3116000-3136200	Strong transcription	Liver	Liver
22	chr4:3116800-3126000	Strong transcription	HepG2	liver
23	chr4:3117000-3125400	Strong transcription	Fetal Brain Female	brain
24	chr4:3117800-3129000	Weak transcription	Psoas Muscle	Psoas
25	chr4:3118200-3128600	Weak transcription	Small Intestine	intestine
26	chr4:3118400-3133600	Weak transcription	Hela-S3	cervix
27	chr4:3118600-3128400	Weak transcription	Fetal Brain Male	brain
28	chr4:3118600-3128800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr4:3118800-3132200	Weak transcription	K562	blood
30	chr4:3119000-3133000	Weak transcription	HMEC	breast
31	chr4:3119800-3128600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr4:3120400-3128600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr4:3120400-3128600	Weak transcription	Spleen	Spleen
34	chr4:3121400-3125400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr4:3121400-3127400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr4:3121600-3126200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:3122000-3130600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:3123000-3125400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr4:3123200-3128400	Weak transcription	A549	lung
40	chr4:3123400-3125200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:3123400-3125400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr4:3123400-3125600	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr4:3123600-3126200	Enhancers	Muscle Satellite Cultured Cells	--
44	chr4:3123800-3126000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:3124000-3125400	Enhancers	Stomach Smooth Muscle	stomach
46	chr4:3124000-3125600	Enhancers	Rectal Smooth Muscle	rectum
47	chr4:3124000-3126400	Enhancers	HSMMtube	muscle
48	chr4:3124000-3128600	Weak transcription	Right Ventricle	heart
49	chr4:3124000-3135400	Weak transcription	Stomach Mucosa	stomach
50	chr4:3124200-3125200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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