Variant report

Variant	rs57875258
Chromosome Location	chr4:3089124-3089125
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3082361..3085504-chr4:3087676..3091805,3	K562	blood:
2	chr4:3075920..3077943-chr4:3087601..3090222,2	K562	blood:
3	chr4:2964499..2967018-chr4:3088885..3091824,2	MCF-7	breast:
4	chr4:3076425..3077993-chr4:3087345..3089440,2	MCF-7	breast:
5	chr4:3083170..3085782-chr4:3088829..3091721,2	K562	blood:

Variant related genes	Relation type
ENSG00000197386	Chromatin interaction
ENSG00000251075	Chromatin interaction
ENSG00000125388	Chromatin interaction
ENSG00000087269	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10002065	0.81[AFR][1000 genomes]
rs10016755	0.92[AFR][1000 genomes]
rs16843857	0.95[AFR][1000 genomes]
rs16843866	0.95[AFR][1000 genomes]
rs16843869	0.85[AFR][1000 genomes]
rs16843871	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16843939	1.00[AMR][1000 genomes]
rs16843945	0.83[AMR][1000 genomes]
rs28580164	0.85[AFR][1000 genomes]
rs28583552	0.92[AFR][1000 genomes]
rs28634516	0.95[AFR][1000 genomes]
rs28652828	0.95[AFR][1000 genomes]
rs28660254	0.92[AFR][1000 genomes]
rs3025838	1.00[AMR][1000 genomes]
rs3025852	1.00[AMR][1000 genomes]
rs3025853	1.00[AMR][1000 genomes]
rs56021098	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56134819	1.00[AMR][1000 genomes]
rs56148664	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57792935	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6830019	0.90[AFR][1000 genomes]
rs6836289	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73792195	0.83[AMR][1000 genomes]
rs7442144	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7667172	1.00[AMR][1000 genomes]
rs7693317	0.86[AFR][1000 genomes]
rs7698150	1.00[AMR][1000 genomes]
rs9996075	0.93[AFR][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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3077400-3093800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:3077800-3096400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:3078000-3094600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:3078000-3094600	Weak transcription	Esophagus	oesophagus
5	chr4:3078000-3097400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:3078000-3097600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr4:3078000-3101000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:3078000-3103000	Weak transcription	Colonic Mucosa	Colon
9	chr4:3078200-3094600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr4:3078200-3101000	Weak transcription	Brain Substantia Nigra	brain
11	chr4:3078200-3109800	Weak transcription	Stomach Mucosa	stomach
12	chr4:3078400-3091600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr4:3078400-3093200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr4:3078400-3094600	Weak transcription	A549	lung
15	chr4:3078400-3097000	Weak transcription	Brain Anterior Caudate	brain
16	chr4:3078400-3102200	Weak transcription	Hela-S3	cervix
17	chr4:3078400-3107000	Weak transcription	HMEC	breast
18	chr4:3078600-3090200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:3078600-3090200	Weak transcription	HSMM	muscle
20	chr4:3078600-3094200	Weak transcription	Fetal Brain Female	brain
21	chr4:3078600-3094200	Weak transcription	Fetal Muscle Leg	muscle
22	chr4:3078600-3094200	Weak transcription	HSMMtube	muscle
23	chr4:3078600-3094600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr4:3078600-3094600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr4:3078600-3101000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr4:3078600-3113800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr4:3078800-3108800	Weak transcription	Psoas Muscle	Psoas
28	chr4:3079000-3094000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr4:3079800-3107200	Weak transcription	Fetal Brain Male	brain
30	chr4:3080000-3090600	Weak transcription	Fetal Kidney	kidney
31	chr4:3080000-3094600	Weak transcription	Brain Germinal Matrix	brain
32	chr4:3080000-3117800	Weak transcription	Small Intestine	intestine
33	chr4:3080200-3093200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr4:3081600-3101000	Weak transcription	Spleen	Spleen
35	chr4:3081800-3093200	Weak transcription	Fetal Heart	heart
36	chr4:3081800-3101600	Weak transcription	Ovary	ovary
37	chr4:3081800-3101600	Weak transcription	Right Ventricle	heart
38	chr4:3084200-3090400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr4:3084200-3097200	Weak transcription	NHDF-Ad	bronchial
40	chr4:3084400-3109000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr4:3084600-3089200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr4:3084600-3093200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr4:3084600-3102000	Weak transcription	Gastric	stomach
44	chr4:3084600-3109000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr4:3085000-3094600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr4:3085600-3107000	Weak transcription	K562	blood
47	chr4:3086200-3089600	Enhancers	Liver	Liver
48	chr4:3086800-3098200	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr4:3087200-3094600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:3087200-3101000	Weak transcription	Pancreas	Pancrea

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