Variant report

Variant	rs9790400
Chromosome Location	chr4:7769828-7769829
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7768892..7770809-chr4:7771728..7774160,2	K562	blood:
2	chr4:7767721..7770258-chr4:7770613..7772876,3	K562	blood:
3	chr4:6934398..6936821-chr4:7767820..7770493,2	K562	blood:
4	chr4:7769826..7772813-chr4:7778014..7779534,2	K562	blood:
5	chr4:7768621..7770539-chr4:7778171..7781125,2	K562	blood:
6	chr4:7764728..7766346-chr4:7767900..7769988,2	K562	blood:

Variant related genes	Relation type
ENSG00000196526	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10516188	0.91[CEU][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10937859	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1106248	0.90[JPT][hapmap]
rs12501415	0.84[EUR][1000 genomes]
rs12505487	0.84[CEU][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12509628	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12511332	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12511919	0.82[CEU][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12512093	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12512166	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16841110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16841121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16841150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16841183	0.91[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16841209	0.91[CEU][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16841268	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16841283	0.82[CEU][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16841288	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2269877	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2285763	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2285768	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34002186	0.84[EUR][1000 genomes]
rs6824231	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs730420	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs73797315	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs877707	0.82[CEU][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9683902	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9790478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv878577	chr4:7757650-7771201	Genic enhancers Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7746200-7772000	Weak transcription	Brain Anterior Caudate	brain
2	chr4:7757000-7772000	Strong transcription	Brain Germinal Matrix	brain
3	chr4:7757600-7770800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:7757600-7779600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:7757800-7772000	Strong transcription	Fetal Intestine Small	intestine
6	chr4:7758000-7780800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:7758200-7783200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:7758400-7795400	Weak transcription	Hela-S3	cervix
9	chr4:7758600-7780600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:7759400-7790400	Weak transcription	Psoas Muscle	Psoas
11	chr4:7759800-7771600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:7759800-7773800	Weak transcription	Fetal Kidney	kidney
13	chr4:7760000-7770000	Strong transcription	Fetal Stomach	stomach
14	chr4:7760000-7783000	Strong transcription	HSMMtube	muscle
15	chr4:7760000-7783200	Strong transcription	HSMM	muscle
16	chr4:7760200-7774200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr4:7760200-7779400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:7760400-7780400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:7760600-7780000	Weak transcription	Right Atrium	heart
20	chr4:7761000-7780400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:7761200-7770600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr4:7761200-7772000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:7761200-7781000	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr4:7761400-7773400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr4:7761400-7784400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:7761800-7774400	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:7762000-7772000	Strong transcription	Fetal Intestine Large	intestine
28	chr4:7762000-7773800	Strong transcription	NHLF	lung
29	chr4:7762000-7788000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:7762000-7805800	Weak transcription	Stomach Mucosa	stomach
31	chr4:7762200-7770200	Strong transcription	Fetal Brain Female	brain
32	chr4:7762200-7771200	Strong transcription	NHEK	skin
33	chr4:7762200-7772800	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr4:7762400-7772200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr4:7763000-7775400	Weak transcription	Right Ventricle	heart
36	chr4:7763400-7770400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr4:7763600-7771000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr4:7763800-7772200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr4:7764000-7772000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr4:7764000-7772200	Weak transcription	Primary T cells from cord blood	blood
41	chr4:7764000-7773400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr4:7764000-7774400	Strong transcription	Adipose Nuclei	Adipose
43	chr4:7764200-7772000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr4:7764400-7770800	Strong transcription	Ovary	ovary
45	chr4:7764400-7771000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr4:7764400-7776400	Strong transcription	Gastric	stomach
47	chr4:7764800-7774400	Strong transcription	Placenta	Placenta
48	chr4:7765000-7772600	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr4:7765000-7776600	Strong transcription	Spleen	Spleen
50	chr4:7765000-7780000	Strong transcription	Lung	lung

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