Variant report

Variant	rs28580164
Chromosome Location	chr4:3102940-3102941
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3075725..3079021-chr4:3101094..3105877,5	MCF-7	breast:
2	chr4:3097049..3099921-chr4:3101807..3103894,2	K562	blood:
3	chr4:3101999..3103736-chr4:3111886..3114032,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251075	Chromatin interaction
ENSG00000197386	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10000252	0.86[EUR][1000 genomes]
rs10002065	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10006129	0.84[EUR][1000 genomes]
rs10006977	0.87[EUR][1000 genomes]
rs10009229	1.00[EUR][1000 genomes]
rs10009935	0.84[EUR][1000 genomes]
rs10011127	1.00[EUR][1000 genomes]
rs10014333	0.87[EUR][1000 genomes]
rs10016755	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10030079	0.86[EUR][1000 genomes]
rs10034313	0.93[EUR][1000 genomes]
rs10222986	0.87[EUR][1000 genomes]
rs1419036	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16843857	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16843866	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16843869	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16843871	0.85[AFR][1000 genomes]
rs28387056	0.93[EUR][1000 genomes]
rs28393280	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28394705	0.84[EUR][1000 genomes]
rs28468636	0.80[EUR][1000 genomes]
rs28485764	0.84[EUR][1000 genomes]
rs28583447	0.80[EUR][1000 genomes]
rs28583552	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28584232	0.84[EUR][1000 genomes]
rs28629394	0.84[EUR][1000 genomes]
rs28634516	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28652828	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28660254	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28670335	0.93[EUR][1000 genomes]
rs28696693	0.87[EUR][1000 genomes]
rs28714390	0.84[EUR][1000 genomes]
rs28718346	0.87[EUR][1000 genomes]
rs28755900	0.90[EUR][1000 genomes]
rs3025836	0.93[EUR][1000 genomes]
rs363138	0.93[EUR][1000 genomes]
rs4346595	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56021098	0.85[AFR][1000 genomes]
rs56148664	0.86[AFR][1000 genomes]
rs57792935	0.86[AFR][1000 genomes]
rs57875258	0.85[AFR][1000 genomes]
rs6830019	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6835897	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6836289	0.86[AFR][1000 genomes]
rs7436457	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7664480	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7693317	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9994689	0.93[EUR][1000 genomes]
rs9995782	0.93[EUR][1000 genomes]
rs9996075	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3078000-3103000	Weak transcription	Colonic Mucosa	Colon
2	chr4:3078200-3109800	Weak transcription	Stomach Mucosa	stomach
3	chr4:3078400-3107000	Weak transcription	HMEC	breast
4	chr4:3078600-3113800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr4:3078800-3108800	Weak transcription	Psoas Muscle	Psoas
6	chr4:3079800-3107200	Weak transcription	Fetal Brain Male	brain
7	chr4:3080000-3117800	Weak transcription	Small Intestine	intestine
8	chr4:3084400-3109000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:3084600-3109000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:3085600-3107000	Weak transcription	K562	blood
11	chr4:3087800-3108800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr4:3088200-3164200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr4:3092400-3108200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr4:3093400-3108800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr4:3093600-3109200	Weak transcription	Fetal Heart	heart
16	chr4:3094400-3123400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr4:3094600-3105000	Strong transcription	Primary B cells from cord blood	blood
18	chr4:3095000-3108200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr4:3095200-3109000	Weak transcription	A549	lung
20	chr4:3095600-3107200	Weak transcription	HSMMtube	muscle
21	chr4:3096400-3108000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:3097000-3108200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr4:3097200-3143400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:3097200-3162200	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:3097400-3107400	Strong transcription	GM12878-XiMat	blood
26	chr4:3097400-3107800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:3097400-3163800	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:3097600-3104600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:3098000-3162600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:3098600-3109800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr4:3099800-3108200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr4:3099800-3108200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr4:3099800-3114400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr4:3100000-3104800	Strong transcription	Dnd41	blood
35	chr4:3100000-3107800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:3100000-3108000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:3100000-3108200	Strong transcription	Primary B cells from peripheral blood	blood
38	chr4:3100000-3110400	Strong transcription	Primary hematopoietic stem cells	blood
39	chr4:3100000-3159400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr4:3100400-3103800	Strong transcription	Brain Germinal Matrix	brain
41	chr4:3100400-3104000	Strong transcription	Rectal Smooth Muscle	rectum
42	chr4:3100400-3104800	Strong transcription	Primary T cells from cord blood	blood
43	chr4:3100400-3112000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:3100600-3104800	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr4:3100600-3106400	Weak transcription	NHDF-Ad	bronchial
46	chr4:3100600-3108000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr4:3100600-3108400	Strong transcription	Fetal Muscle Trunk	muscle
48	chr4:3100800-3103400	Strong transcription	Placenta	Placenta
49	chr4:3100800-3103600	Strong transcription	Fetal Lung	lung
50	chr4:3100800-3104400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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