Variant report

Variant	rs7664100
Chromosome Location	chr4:56222599-56222600
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:56211148..56230966-chr4:56256626..56269458,54	MCF-7	breast:
2	chr4:56220332..56223664-chr4:56260663..56265029,5	K562	blood:
3	chr4:56222589..56224784-chr4:56242075..56244451,2	K562	blood:
4	chr4:56221079..56223378-chr4:56272404..56274272,2	MCF-7	breast:
5	chr4:56209954..56216628-chr4:56219638..56226284,12	MCF-7	breast:
6	chr4:56217504..56220153-chr4:56221676..56223372,2	MCF-7	breast:
7	chr4:56222050..56228109-chr4:56258616..56264786,10	MCF-7	breast:
8	chr4:56221889..56224651-chr4:56225282..56227252,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000134851	Chromatin interaction
ENSG00000249700	Chromatin interaction
ENSG00000251111	Chromatin interaction
ENSG00000128039	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10001607	0.82[CEU][hapmap]
rs10001859	0.82[EUR][1000 genomes]
rs11133375	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11133386	0.80[YRI][hapmap]
rs11943456	0.83[MEX][hapmap];0.80[TSI][hapmap]
rs12650678	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13124164	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1985606	0.92[CEU][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2063577	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2538	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs4864982	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs576732	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs6813878	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6835891	0.92[EUR][1000 genomes]
rs7672248	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs819266	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs819268	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs819269	0.89[CHB][hapmap]
rs819270	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs9790808	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[CHD][hapmap];0.80[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[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	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7664100	TMEM165	cis	parietal	SCAN
rs7664100	TMEM165	cis	Nerve Tibial	GTEx
rs7664100	TMEM165	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56213200-56230000	Weak transcription	Fetal Kidney	kidney
2	chr4:56213400-56223800	Weak transcription	Fetal Heart	heart
3	chr4:56213400-56225400	Weak transcription	Spleen	Spleen
4	chr4:56213400-56233600	Weak transcription	Fetal Intestine Large	intestine
5	chr4:56213600-56223000	Weak transcription	Esophagus	oesophagus
6	chr4:56213600-56223000	Weak transcription	HSMM	muscle
7	chr4:56213600-56224000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:56213600-56225600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr4:56213600-56229200	Weak transcription	Fetal Intestine Small	intestine
10	chr4:56213600-56230200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:56213600-56230200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr4:56213600-56242600	Weak transcription	Gastric	stomach
13	chr4:56213800-56223000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr4:56213800-56225200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr4:56213800-56225600	Weak transcription	Left Ventricle	heart
16	chr4:56213800-56227000	Weak transcription	Placenta	Placenta
17	chr4:56213800-56229800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr4:56213800-56229800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr4:56213800-56229800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr4:56213800-56231800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr4:56213800-56233600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr4:56213800-56239000	Weak transcription	Brain Germinal Matrix	brain
23	chr4:56213800-56251400	Weak transcription	Pancreas	Pancrea
24	chr4:56214000-56223400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr4:56214000-56224600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr4:56214000-56225600	Weak transcription	Fetal Muscle Leg	muscle
27	chr4:56214000-56229800	Weak transcription	Liver	Liver
28	chr4:56214000-56229800	Weak transcription	Fetal Thymus	thymus
29	chr4:56214000-56229800	Weak transcription	Thymus	Thymus
30	chr4:56214000-56230200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr4:56214000-56231000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr4:56214000-56237800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr4:56214000-56241800	Weak transcription	Colonic Mucosa	Colon
34	chr4:56214200-56222600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:56214200-56224800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr4:56214400-56247600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr4:56214600-56224200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr4:56214600-56230200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr4:56214800-56225000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:56215000-56222600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:56215000-56223400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr4:56215000-56224200	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr4:56215000-56224400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr4:56215000-56225400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr4:56215000-56227400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr4:56215000-56229800	Weak transcription	Brain Angular Gyrus	brain
47	chr4:56215000-56235400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr4:56215200-56223000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:56215200-56223000	Weak transcription	Osteobl	bone
50	chr4:56215200-56225000	Weak transcription	Brain Hippocampus Middle	brain

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