Variant report

Variant	rs1675531
Chromosome Location	chr3:98310872-98310873
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98240168..98242320-chr3:98310651..98312763,2	K562	blood:
2	chr3:98302949..98305459-chr3:98308547..98310946,2	K562	blood:

Variant related genes	Relation type
ENSG00000080822	Chromatin interaction
ENSG00000248839	Chromatin interaction
ENSG00000080819	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10222524	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1350792	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1350793	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1381090	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1675526	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1675527	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1675528	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1729978	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1729980	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1729995	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2698315	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34330560	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3762654	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3853723	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4558798	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528056	chr3:98101101-98317836	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv520503	chr3:98102801-98317836	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv834775	chr3:98170059-98367552	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv997484	chr3:98284283-98371420	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1000357	chr3:98284283-98381473	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv536661	chr3:98286588-98315764	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98292400-98311000	Weak transcription	Fetal Brain Male	brain
2	chr3:98293000-98311800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:98294400-98311000	Weak transcription	Stomach Mucosa	stomach
4	chr3:98294800-98311000	Weak transcription	Esophagus	oesophagus
5	chr3:98296600-98311200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:98299600-98311200	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr3:98300000-98311200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:98304400-98311600	Weak transcription	Aorta	Aorta
9	chr3:98304600-98311400	Weak transcription	HSMMtube	muscle
10	chr3:98304800-98311000	Weak transcription	HSMM	muscle
11	chr3:98305000-98311600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:98305200-98311000	Weak transcription	Spleen	Spleen
13	chr3:98305200-98311600	Weak transcription	Gastric	stomach
14	chr3:98305400-98311000	Weak transcription	Thymus	Thymus
15	chr3:98305600-98311000	Weak transcription	Right Ventricle	heart
16	chr3:98307000-98311000	Weak transcription	A549	lung
17	chr3:98308400-98311000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:98308800-98311000	Weak transcription	Primary B cells from cord blood	blood
19	chr3:98308800-98311000	Weak transcription	Fetal Kidney	kidney
20	chr3:98308800-98311000	Weak transcription	Psoas Muscle	Psoas
21	chr3:98309000-98311000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:98309000-98311000	Weak transcription	Osteobl	bone
23	chr3:98309400-98311000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:98309400-98311000	Weak transcription	Fetal Stomach	stomach
25	chr3:98309400-98311200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:98309600-98311000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:98309600-98311000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:98309600-98311000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:98309600-98311000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:98309600-98311000	Active TSS	Brain Cingulate Gyrus	brain
31	chr3:98309600-98311000	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr3:98309600-98311000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr3:98309600-98311000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:98309600-98311000	Weak transcription	Fetal Muscle Leg	muscle
35	chr3:98309600-98311000	Weak transcription	Fetal Thymus	thymus
36	chr3:98309600-98311000	Weak transcription	Pancreas	Pancrea
37	chr3:98309600-98311000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr3:98309600-98311000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:98309600-98311000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr3:98309600-98311400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr3:98309600-98311400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr3:98309600-98311600	Weak transcription	Lung	lung
43	chr3:98309800-98311000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:98309800-98311000	Weak transcription	NHDF-Ad	bronchial
45	chr3:98309800-98311200	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr3:98310000-98311000	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr3:98310000-98311000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:98310000-98311000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:98310000-98311000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:98310000-98311000	Weak transcription	Primary T cells fromperipheralblood	blood

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