Variant report

Variant	rs3798115
Chromosome Location	chr5:128441640-128441641
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:128429052..128430822-chr5:128440263..128442695,2	K562	blood:
2	chr5:128438665..128441668-chr5:128448415..128451376,3	K562	blood:
3	chr5:128429310..128432556-chr5:128440701..128444260,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066583	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10036277	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10058170	0.81[AMR][1000 genomes]
rs10071265	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1127827	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1148739	0.80[CEU][hapmap]
rs1181978	0.80[CEU][hapmap]
rs1181979	0.80[CEU][hapmap]
rs1186251	0.80[CEU][hapmap]
rs11960471	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13181777	0.80[CEU][hapmap]
rs2112697	0.87[AMR][1000 genomes]
rs2161403	0.84[AMR][1000 genomes]
rs2194149	0.83[AMR][1000 genomes]
rs2312251	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2430194	0.96[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2430195	0.96[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs257911	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs257912	0.95[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs257919	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3798116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3798117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3798120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822830	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3822832	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4141014	0.80[CEU][hapmap]
rs4836444	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58498861	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6595879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6595885	0.84[AMR][1000 genomes]
rs6867600	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6868228	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881138	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6888909	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7714427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7733245	0.83[AMR][1000 genomes]
rs963677	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830485	chr5:128298622-128480492	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv882842	chr5:128301971-128552706	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv599701	chr5:128328165-128773052	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1015525	chr5:128335133-128443859	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv882847	chr5:128368505-128665719	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
6	nsv882848	chr5:128378225-128516629	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 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	chr5:128431200-128447800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:128431400-128443600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr5:128431400-128450600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:128431400-128457400	Weak transcription	Lung	lung
5	chr5:128431600-128442000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr5:128431600-128442000	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr5:128431600-128442600	Weak transcription	Thymus	Thymus
8	chr5:128431600-128444000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:128431600-128446000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:128431600-128446400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:128431600-128450400	Weak transcription	Placenta	Placenta
12	chr5:128431600-128450400	Weak transcription	HSMM	muscle
13	chr5:128431600-128454200	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr5:128431800-128446400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr5:128432200-128442400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:128432200-128442600	Weak transcription	A549	lung
17	chr5:128432200-128442800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:128432200-128450400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr5:128432200-128454600	Weak transcription	Aorta	Aorta
20	chr5:128432400-128442200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr5:128432400-128442600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:128432400-128442600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:128432400-128446000	Weak transcription	HMEC	breast
24	chr5:128432400-128450400	Weak transcription	Brain Angular Gyrus	brain
25	chr5:128432600-128442200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr5:128432600-128442600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:128433400-128453800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr5:128433800-128441800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr5:128433800-128442600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr5:128434000-128443200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr5:128434000-128444200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr5:128434000-128448800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr5:128434000-128455600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr5:128434000-128458400	Weak transcription	Esophagus	oesophagus
35	chr5:128434200-128446200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr5:128434200-128446400	Weak transcription	Brain Hippocampus Middle	brain
37	chr5:128434400-128441800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:128434400-128442200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr5:128434400-128442600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr5:128434400-128447000	Weak transcription	Colon Smooth Muscle	Colon
41	chr5:128434400-128454200	Weak transcription	Colonic Mucosa	Colon
42	chr5:128434400-128461800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr5:128434600-128442000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr5:128434600-128445600	Weak transcription	Small Intestine	intestine
45	chr5:128434800-128441800	Weak transcription	Fetal Intestine Large	intestine
46	chr5:128434800-128442200	Weak transcription	Primary T cells from cord blood	blood
47	chr5:128434800-128442200	Weak transcription	Fetal Muscle Leg	muscle
48	chr5:128434800-128442600	Weak transcription	Gastric	stomach
49	chr5:128434800-128443800	Weak transcription	Fetal Intestine Small	intestine
50	chr5:128434800-128446400	Weak transcription	Muscle Satellite Cultured Cells	--

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