Variant report

Variant	rs28641865
Chromosome Location	chr7:150437393-150437394
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	chr7:150433868..150435484-chr7:150436619..150439022,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GIMAP5-1	chr7:150437105-150437592	NONHSAT124152

Variant related genes	Relation type
ENSG00000196329	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10239400	0.90[ASN][1000 genomes]
rs10242011	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10271868	0.81[ASN][1000 genomes]
rs10361	0.89[ASN][1000 genomes]
rs1046355	0.90[ASN][1000 genomes]
rs11760839	0.82[ASN][1000 genomes]
rs12703098	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17173582	0.82[ASN][1000 genomes]
rs2286898	0.89[ASN][1000 genomes]
rs2286899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28418764	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28505524	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34078863	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34443555	0.92[ASN][1000 genomes]
rs34906783	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35112724	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35257925	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4725937	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57024360	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62490401	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62490403	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6598	0.89[ASN][1000 genomes]
rs6980405	0.83[ASN][1000 genomes]
rs759011	0.90[ASN][1000 genomes]
rs7807580	0.82[ASN][1000 genomes]
rs9657886	0.93[ASN][1000 genomes]
rs9657890	0.92[ASN][1000 genomes]
rs9657894	0.92[ASN][1000 genomes]
rs9657898	0.90[ASN][1000 genomes]
rs9657900	0.90[ASN][1000 genomes]
rs9969148	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9969242	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9969243	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9969309	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	esv2758617	chr7:150251949-150463804	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2759573	chr7:150251949-150463804	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv1030109	chr7:150312916-150701010	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv967475	chr7:150323577-150610034	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv831187	chr7:150325913-150503500	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150433800-150439200	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr7:150434000-150437400	Active TSS	Brain Anterior Caudate	brain
3	chr7:150434000-150437400	Active TSS	Colonic Mucosa	Colon
4	chr7:150434000-150437600	Active TSS	Lung	lung
5	chr7:150434000-150437600	Active TSS	Rectal Mucosa Donor 31	rectum
6	chr7:150434000-150437600	Active TSS	Right Ventricle	heart
7	chr7:150434000-150437800	Active TSS	Rectal Smooth Muscle	rectum
8	chr7:150434000-150438000	Active TSS	Right Atrium	heart
9	chr7:150434200-150437400	Active TSS	Primary T cells fromperipheralblood	blood
10	chr7:150434200-150437600	Active TSS	Brain Hippocampus Middle	brain
11	chr7:150434200-150437600	Active TSS	Left Ventricle	heart
12	chr7:150434200-150437600	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr7:150434200-150437800	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr7:150434200-150437800	Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr7:150434200-150438000	Active TSS	Duodenum Mucosa	Duodenum
16	chr7:150434200-150438000	Active TSS	Psoas Muscle	Psoas
17	chr7:150434400-150437400	Active TSS	Brain Angular Gyrus	brain
18	chr7:150434400-150437400	Active TSS	Thymus	Thymus
19	chr7:150434400-150437800	Active TSS	Adipose Nuclei	Adipose
20	chr7:150434600-150440600	Transcr. at gene 5' and 3'	Dnd41	blood
21	chr7:150434800-150437400	Active TSS	Primary B cells from cord blood	blood
22	chr7:150434800-150437400	Enhancers	HMEC	breast
23	chr7:150435000-150437800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr7:150435200-150437600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
25	chr7:150435200-150437600	Active TSS	Stomach Smooth Muscle	stomach
26	chr7:150435400-150437400	Flanking Active TSS	Liver	Liver
27	chr7:150435400-150437600	Active TSS	Fetal Muscle Leg	muscle
28	chr7:150435400-150439000	Active TSS	GM12878-XiMat	blood
29	chr7:150435400-150442800	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
30	chr7:150435600-150437600	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr7:150435600-150442400	Weak transcription	Ovary	ovary
32	chr7:150435800-150437800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr7:150435800-150439600	Weak transcription	Colon Smooth Muscle	Colon
34	chr7:150435800-150441000	Weak transcription	Pancreas	Pancrea
35	chr7:150435800-150441200	Weak transcription	Gastric	stomach
36	chr7:150435800-150441800	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
37	chr7:150436000-150441800	Weak transcription	Fetal Intestine Small	intestine
38	chr7:150436200-150437400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr7:150436200-150439600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr7:150436200-150450200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr7:150436400-150439600	Weak transcription	Fetal Muscle Trunk	muscle
42	chr7:150436400-150443400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
43	chr7:150436800-150438000	Weak transcription	Placenta	Placenta
44	chr7:150436800-150438200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr7:150436800-150442200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
46	chr7:150436800-150451400	Weak transcription	Brain Substantia Nigra	brain
47	chr7:150437000-150437400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr7:150437000-150438000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:150437000-150439800	Weak transcription	Fetal Heart	heart
50	chr7:150437000-150441600	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood

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