Variant report

Variant	rs28387056
Chromosome Location	chr4:3091198-3091199
allele	G/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	chr4:2964499..2967018-chr4:3088885..3091824,2	MCF-7	breast:
3	chr4:3076858..3078560-chr4:3090552..3093969,4	MCF-7	breast:
4	chr4:3083170..3085782-chr4:3088829..3091721,2	K562	blood:

Variant related genes	Relation type
ENSG00000125388	Chromatin interaction
ENSG00000087269	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10002065	0.93[EUR][1000 genomes]
rs10006129	0.90[EUR][1000 genomes]
rs10006977	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10009229	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10009935	0.90[EUR][1000 genomes]
rs10011127	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10014333	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10016755	0.93[EUR][1000 genomes]
rs10034313	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10222986	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1419036	0.93[EUR][1000 genomes]
rs16843857	0.93[EUR][1000 genomes]
rs16843866	0.93[EUR][1000 genomes]
rs16843869	0.93[EUR][1000 genomes]
rs28393280	1.00[EUR][1000 genomes]
rs28394705	0.90[EUR][1000 genomes]
rs28468636	0.87[EUR][1000 genomes]
rs28485764	0.90[EUR][1000 genomes]
rs28564368	0.81[EUR][1000 genomes]
rs28580164	0.93[EUR][1000 genomes]
rs28583447	0.87[EUR][1000 genomes]
rs28583552	0.90[EUR][1000 genomes]
rs28584232	0.90[EUR][1000 genomes]
rs28629394	0.90[EUR][1000 genomes]
rs28634516	0.93[EUR][1000 genomes]
rs28652828	0.84[EUR][1000 genomes]
rs28660254	0.93[EUR][1000 genomes]
rs28670335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28682489	0.84[EUR][1000 genomes]
rs28696693	0.93[EUR][1000 genomes]
rs28714390	0.90[EUR][1000 genomes]
rs28718346	0.93[EUR][1000 genomes]
rs28755900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3025836	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs363138	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4346595	1.00[EUR][1000 genomes]
rs6830019	1.00[EUR][1000 genomes]
rs6835897	1.00[EUR][1000 genomes]
rs7436457	1.00[EUR][1000 genomes]
rs7664480	1.00[EUR][1000 genomes]
rs7693317	0.93[EUR][1000 genomes]
rs9994689	0.87[EUR][1000 genomes]
rs9995782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9996075	1.00[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: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	chr4:3078600-3094200	Weak transcription	Fetal Brain Female	brain
19	chr4:3078600-3094200	Weak transcription	Fetal Muscle Leg	muscle
20	chr4:3078600-3094200	Weak transcription	HSMMtube	muscle
21	chr4:3078600-3094600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:3078600-3094600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr4:3078600-3101000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr4:3078600-3113800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr4:3078800-3108800	Weak transcription	Psoas Muscle	Psoas
26	chr4:3079000-3094000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr4:3079800-3107200	Weak transcription	Fetal Brain Male	brain
28	chr4:3080000-3094600	Weak transcription	Brain Germinal Matrix	brain
29	chr4:3080000-3117800	Weak transcription	Small Intestine	intestine
30	chr4:3080200-3093200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:3081600-3101000	Weak transcription	Spleen	Spleen
32	chr4:3081800-3093200	Weak transcription	Fetal Heart	heart
33	chr4:3081800-3101600	Weak transcription	Ovary	ovary
34	chr4:3081800-3101600	Weak transcription	Right Ventricle	heart
35	chr4:3084200-3097200	Weak transcription	NHDF-Ad	bronchial
36	chr4:3084400-3109000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr4:3084600-3093200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr4:3084600-3102000	Weak transcription	Gastric	stomach
39	chr4:3084600-3109000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr4:3085000-3094600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr4:3085600-3107000	Weak transcription	K562	blood
42	chr4:3086800-3098200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr4:3087200-3094600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:3087200-3101000	Weak transcription	Pancreas	Pancrea
45	chr4:3087400-3095600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr4:3087400-3101800	Weak transcription	NHEK	skin
47	chr4:3087800-3091400	Strong transcription	Primary B cells from cord blood	blood
48	chr4:3087800-3094600	Strong transcription	Dnd41	blood
49	chr4:3087800-3108800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr4:3088000-3094200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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