Variant report

Variant	rs1729978
Chromosome Location	chr3:98310190-98310191
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	chr3:98302949..98305459-chr3:98308547..98310946,2	K562	blood:

Variant related genes	Relation type
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	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1350792	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1350793	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1381090	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1675526	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1675527	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1675528	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1675531	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1729980	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1729995	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2698315	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34330560	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3762654	0.88[EUR][1000 genomes]
rs3853723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4558798	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98287200-98310200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr3:98287400-98310400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr3:98292400-98310400	Weak transcription	Small Intestine	intestine
4	chr3:98292400-98311000	Weak transcription	Fetal Brain Male	brain
5	chr3:98292600-98310200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:98293000-98311800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:98293200-98310400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:98294400-98310400	Weak transcription	Colonic Mucosa	Colon
9	chr3:98294400-98311000	Weak transcription	Stomach Mucosa	stomach
10	chr3:98294800-98311000	Weak transcription	Esophagus	oesophagus
11	chr3:98296000-98310200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:98296200-98310400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:98296600-98311200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:98296800-98310800	Weak transcription	NHLF	lung
15	chr3:98297400-98310400	Weak transcription	Hela-S3	cervix
16	chr3:98298200-98310800	Weak transcription	HUVEC	blood vessel
17	chr3:98299600-98311200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr3:98300000-98311200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:98302400-98310200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:98302600-98310200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:98302600-98310200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:98303800-98310200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr3:98304400-98311600	Weak transcription	Aorta	Aorta
24	chr3:98304600-98310600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:98304600-98310800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:98304600-98311400	Weak transcription	HSMMtube	muscle
27	chr3:98304800-98310200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr3:98304800-98311000	Weak transcription	HSMM	muscle
29	chr3:98305000-98311600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:98305200-98311000	Weak transcription	Spleen	Spleen
31	chr3:98305200-98311600	Weak transcription	Gastric	stomach
32	chr3:98305400-98311000	Weak transcription	Thymus	Thymus
33	chr3:98305600-98311000	Weak transcription	Right Ventricle	heart
34	chr3:98305800-98310400	Weak transcription	Fetal Intestine Small	intestine
35	chr3:98307000-98311000	Weak transcription	A549	lung
36	chr3:98307400-98310200	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr3:98307600-98310200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:98307600-98310200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
39	chr3:98307800-98310200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr3:98307800-98310200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:98307800-98310400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:98308400-98310200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:98308400-98311000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:98308600-98310200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:98308600-98310200	Strong transcription	Rectal Smooth Muscle	rectum
46	chr3:98308800-98310200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr3:98308800-98310400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:98308800-98310400	Weak transcription	Fetal Intestine Large	intestine
49	chr3:98308800-98310600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:98308800-98311000	Weak transcription	Primary B cells from cord blood	blood

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