Variant report

Variant	rs3108180
Chromosome Location	chr19:37188952-37188953
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37176901..37179130-chr19:37188075..37189594,2	K562	blood:
2	chr19:37176901..37179127-chr19:37187369..37189594,2	K562	blood:

Variant related genes	Relation type
ENSG00000189042	Chromatin interaction
ENSG00000225975	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10411411	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1053064	0.97[EUR][1000 genomes]
rs12162275	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12973307	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2385640	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2462576	0.87[ASN][1000 genomes]
rs2912401	0.88[EUR][1000 genomes]
rs2912402	0.87[EUR][1000 genomes]
rs2912406	0.89[EUR][1000 genomes]
rs2912416	0.89[EUR][1000 genomes]
rs2912417	0.88[EUR][1000 genomes]
rs2967424	0.86[EUR][1000 genomes]
rs2967455	0.89[EUR][1000 genomes]
rs2967470	0.89[EUR][1000 genomes]
rs3096621	0.89[EUR][1000 genomes]
rs3096626	0.81[EUR][1000 genomes]
rs3108169	0.90[EUR][1000 genomes]
rs3108170	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108175	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108198	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108199	0.96[EUR][1000 genomes]
rs3108200	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108207	0.97[EUR][1000 genomes]
rs3108213	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108220	0.84[ASN][1000 genomes]
rs3108547	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108548	0.88[EUR][1000 genomes]
rs3108551	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108553	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108554	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3108558	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108561	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108571	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108578	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108581	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108582	0.88[ASN][1000 genomes]
rs3108587	0.85[EUR][1000 genomes]
rs3108588	0.88[ASN][1000 genomes]
rs3108595	0.89[EUR][1000 genomes]
rs3108599	0.88[EUR][1000 genomes]
rs3108601	0.89[EUR][1000 genomes]
rs3108611	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3111543	0.89[EUR][1000 genomes]
rs3111545	0.88[EUR][1000 genomes]
rs3111546	0.89[EUR][1000 genomes]
rs71337534	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7254978	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8112546	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs826979	0.83[ASN][1000 genomes]
rs826980	0.84[ASN][1000 genomes]
rs826986	0.88[ASN][1000 genomes]
rs865448	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
7	esv3492171	chr19:37122012-37190210	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
8	esv3492172	chr19:37122562-37190060	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
9	esv3492173	chr19:37122562-37190060	Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
10	nsv469794	chr19:37129858-37310257	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv482392	chr19:37129858-37310257	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers 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	27 gene(s)	inside rSNPs	diseases
12	esv3420176	chr19:37130161-37207917	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
13	esv34384	chr19:37134068-37330613	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
14	nsv817833	chr19:37146694-37357289	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
15	nsv470139	chr19:37171201-37264190	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3108180	ZNF529	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37179400-37194800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:37179400-37199200	Weak transcription	Fetal Heart	heart
3	chr19:37179600-37194400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:37179800-37189000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
5	chr19:37179800-37189000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr19:37179800-37189200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:37180000-37189200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:37180200-37189000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr19:37183600-37203200	Weak transcription	K562	blood
10	chr19:37183800-37189000	ZNF genes & repeats	Fetal Intestine Large	intestine
11	chr19:37184000-37194600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr19:37184400-37194600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:37184400-37199000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr19:37185000-37189200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
15	chr19:37186000-37190000	Weak transcription	Hela-S3	cervix
16	chr19:37186000-37194600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr19:37186200-37189400	Weak transcription	Fetal Thymus	thymus
18	chr19:37186400-37189000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:37186400-37194400	Weak transcription	Thymus	Thymus
20	chr19:37186600-37194400	Weak transcription	Fetal Stomach	stomach
21	chr19:37186600-37195400	Weak transcription	Right Ventricle	heart
22	chr19:37187600-37190400	Weak transcription	HSMMtube	muscle
23	chr19:37187600-37194400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr19:37187600-37194400	Weak transcription	Ovary	ovary
25	chr19:37187600-37194600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:37187600-37194600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr19:37187600-37194600	Weak transcription	Esophagus	oesophagus
28	chr19:37187600-37194600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr19:37187600-37194800	Weak transcription	Gastric	stomach
30	chr19:37187600-37196800	Weak transcription	Brain Angular Gyrus	brain
31	chr19:37187600-37198400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:37187800-37189000	Weak transcription	Fetal Muscle Leg	muscle
33	chr19:37187800-37190000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr19:37187800-37190600	Weak transcription	Brain Substantia Nigra	brain
35	chr19:37187800-37194600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr19:37187800-37194600	Weak transcription	Brain Hippocampus Middle	brain
37	chr19:37188000-37189800	Weak transcription	NHDF-Ad	bronchial
38	chr19:37188000-37195800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr19:37188000-37196400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr19:37188200-37190000	Weak transcription	HSMM	muscle
41	chr19:37188400-37189000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr19:37188400-37189000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr19:37188400-37190200	Weak transcription	Osteobl	bone
44	chr19:37188400-37194600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr19:37188400-37197000	Weak transcription	Fetal Kidney	kidney
46	chr19:37188600-37189000	Weak transcription	Primary B cells from cord blood	blood
47	chr19:37188600-37190800	Weak transcription	Primary B cells from peripheral blood	blood
48	chr19:37188600-37194400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr19:37188600-37194600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr19:37188800-37189200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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