Variant report

Variant	rs61689858
Chromosome Location	chr3:50410149-50410150
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	chr3:50402409..50404056-chr3:50409776..50411818,2	K562	blood:
2	chr3:50387777..50390852-chr3:50409730..50411356,3	K562	blood:

Variant related genes	Relation type
ENSG00000272104	Chromatin interaction
ENSG00000271858	Chromatin interaction
ENSG00000114388	Chromatin interaction
ENSG00000007402	Chromatin interaction
ENSG00000114395	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12485286	0.84[AFR][1000 genomes]
rs2233482	1.00[AMR][1000 genomes]
rs58780990	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59556423	1.00[AMR][1000 genomes]
rs60983897	1.00[AMR][1000 genomes]
rs61275090	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61737738	1.00[AMR][1000 genomes]
rs72932956	1.00[AMR][1000 genomes]
rs72932962	1.00[AMR][1000 genomes]
rs72932964	1.00[AMR][1000 genomes]
rs72932983	1.00[AMR][1000 genomes]
rs72934803	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934806	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934809	0.89[AFR][1000 genomes]
rs72934811	0.81[AFR][1000 genomes]
rs72934814	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934815	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934824	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934827	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934830	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs928946	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
6	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
8	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
9	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
10	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
11	nsv590256	chr3:50302830-50420554	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
12	nsv876774	chr3:50302830-50436827	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
13	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
14	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
15	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
16	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
17	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
18	nsv590259	chr3:50408398-50411819	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50403200-50417200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:50404200-50410600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:50404600-50415400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:50405000-50416400	Weak transcription	Gastric	stomach
5	chr3:50405800-50411200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:50406000-50411000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:50407200-50410600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:50407400-50413400	Enhancers	Brain Germinal Matrix	brain
9	chr3:50407600-50411000	Enhancers	Fetal Muscle Leg	muscle
10	chr3:50408000-50410200	Enhancers	K562	blood
11	chr3:50408200-50410800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:50408200-50411000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:50408200-50411000	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr3:50408400-50410800	Enhancers	H1 Cell Line	embryonic stem cell
15	chr3:50408400-50411400	Enhancers	Fetal Stomach	stomach
16	chr3:50408400-50413200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:50408600-50413000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:50408800-50410200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:50408800-50410400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:50408800-50411000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr3:50408800-50412000	Weak transcription	Lung	lung
22	chr3:50408800-50413000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:50408800-50423800	Weak transcription	Fetal Brain Female	brain
24	chr3:50409000-50419600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:50409200-50420200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:50409400-50410600	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr3:50409400-50410800	Enhancers	A549	lung
28	chr3:50409400-50412200	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr3:50409400-50412800	Enhancers	Fetal Thymus	thymus
30	chr3:50409600-50410200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
31	chr3:50409600-50410200	Enhancers	Duodenum Mucosa	Duodenum
32	chr3:50409600-50410400	Enhancers	Fetal Intestine Large	intestine
33	chr3:50409600-50410400	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr3:50409600-50410400	Bivalent Enhancer	HepG2	liver
35	chr3:50409600-50410800	Enhancers	Fetal Intestine Small	intestine
36	chr3:50409600-50410800	Enhancers	Fetal Muscle Trunk	muscle
37	chr3:50409600-50411200	Enhancers	Primary hematopoietic stem cells	blood
38	chr3:50409600-50411400	Enhancers	Fetal Brain Male	brain
39	chr3:50409800-50410200	Enhancers	Colonic Mucosa	Colon
40	chr3:50409800-50410200	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr3:50409800-50410200	Bivalent Enhancer	Stomach Mucosa	stomach
42	chr3:50409800-50410200	Enhancers	Spleen	Spleen
43	chr3:50409800-50410400	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr3:50409800-50410400	Enhancers	Thymus	Thymus
45	chr3:50409800-50410600	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr3:50409800-50410600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr3:50409800-50411000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr3:50409800-50411600	Enhancers	Primary T cells from cord blood	blood
49	chr3:50409800-50412200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr3:50409800-50412600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links