Variant report

Variant	rs4725359
Chromosome Location	chr7:150438138-150438139
allele	A/G
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:

Variant related genes	Relation type
ENSG00000196329	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10952286	0.92[ASN][1000 genomes]
rs2058448	0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2058449	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3807383	0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs59953726	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6952662	0.92[ASN][1000 genomes]
rs6955828	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6960420	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6972456	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9657876	0.82[ASN][1000 genomes]
rs9657901	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4725359	VIM	trans	lymphoblastoid	seeQTL
rs4725359	GIMAP6	Cis_1M	lymphoblastoid	RTeQTL
rs4725359	ABCB8	cis	cerebellum	SCAN
rs4725359	GIMAP5	cis	cerebellum	SCAN

Chromatin state (count:59 , 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	chr7:150434600-150440600	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr7:150435400-150439000	Active TSS	GM12878-XiMat	blood
4	chr7:150435400-150442800	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
5	chr7:150435600-150442400	Weak transcription	Ovary	ovary
6	chr7:150435800-150439600	Weak transcription	Colon Smooth Muscle	Colon
7	chr7:150435800-150441000	Weak transcription	Pancreas	Pancrea
8	chr7:150435800-150441200	Weak transcription	Gastric	stomach
9	chr7:150435800-150441800	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
10	chr7:150436000-150441800	Weak transcription	Fetal Intestine Small	intestine
11	chr7:150436200-150439600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:150436200-150450200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr7:150436400-150439600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr7:150436400-150443400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
15	chr7:150436800-150438200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr7:150436800-150442200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
17	chr7:150436800-150451400	Weak transcription	Brain Substantia Nigra	brain
18	chr7:150437000-150439800	Weak transcription	Fetal Heart	heart
19	chr7:150437000-150441600	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
20	chr7:150437000-150450000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr7:150437200-150438200	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
22	chr7:150437200-150441400	Transcr. at gene 5' and 3'	Primary T killer naive cells fromperipheralblood	blood
23	chr7:150437200-150441600	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr7:150437200-150441600	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
25	chr7:150437200-150442400	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 2	blood
26	chr7:150437200-150442400	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
27	chr7:150437200-150442600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
28	chr7:150437200-150443200	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
29	chr7:150437400-150439600	Strong transcription	Fetal Thymus	thymus
30	chr7:150437400-150441400	Weak transcription	Colonic Mucosa	Colon
31	chr7:150437400-150441800	Weak transcription	Thymus	Thymus
32	chr7:150437400-150443000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
33	chr7:150437400-150443200	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
34	chr7:150437600-150438600	Weak transcription	Right Ventricle	heart
35	chr7:150437600-150438800	Weak transcription	Fetal Muscle Leg	muscle
36	chr7:150437600-150439000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr7:150437600-150439000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr7:150437600-150439400	Weak transcription	Fetal Stomach	stomach
39	chr7:150437600-150439400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr7:150437600-150439600	Weak transcription	Esophagus	oesophagus
41	chr7:150437600-150439800	Weak transcription	Brain Hippocampus Middle	brain
42	chr7:150437600-150443200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr7:150437600-150443800	Weak transcription	Small Intestine	intestine
44	chr7:150437800-150438200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr7:150437800-150439600	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr7:150437800-150439600	Weak transcription	Liver	Liver
47	chr7:150437800-150439600	Weak transcription	Rectal Smooth Muscle	rectum
48	chr7:150437800-150439800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr7:150438000-150438200	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr7:150438000-150438600	Strong transcription	Lung	lung

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