Variant report

Variant	rs7249636
Chromosome Location	chr19:21556754-21556755
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF708-6	chr19:21555198-21557246	ucscGeneNc_uc002nqf_1

Extended variants
information (count: 77 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1012040	0.81[YRI][hapmap]
rs1055753	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs11085441	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs11085447	0.94[CHB][hapmap];0.98[CHD][hapmap];0.85[JPT][hapmap]
rs11667770	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs12975081	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs12975981	0.86[CEU][hapmap]
rs12981564	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs12981735	0.94[CHB][hapmap]
rs12981869	0.86[CEU][hapmap]
rs12982282	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs1401926	0.81[CHD][hapmap]
rs1678822	1.00[CEU][hapmap]
rs17618778	0.86[CEU][hapmap]
rs1781873	0.89[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap]
rs1813234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs2012013	0.94[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2088762	0.94[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2133816	0.83[YRI][hapmap]
rs2170024	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2173724	0.86[YRI][hapmap]
rs2246914	0.88[YRI][hapmap]
rs2358984	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs2562435	0.81[JPT][hapmap]
rs2650798	0.81[JPT][hapmap]
rs2650845	0.86[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs2681371	0.88[YRI][hapmap]
rs2681372	0.83[YRI][hapmap]
rs2914636	1.00[CEU][hapmap]
rs2914638	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2914645	0.80[JPT][hapmap]
rs2937174	0.81[JPT][hapmap]
rs2968045	0.81[JPT][hapmap]
rs4315457	0.94[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs4341872	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs4621113	0.89[CHB][hapmap];0.80[JPT][hapmap]
rs488125	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs501647	1.00[CEU][hapmap]
rs504280	0.95[CEU][hapmap];0.83[TSI][hapmap]
rs509540	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs566230	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs629548	0.90[CEU][hapmap]
rs6511239	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs669046	0.91[CEU][hapmap]
rs685844	1.00[CEU][hapmap]
rs7247411	0.94[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs7248601	0.86[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap]
rs7249412	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs7252254	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs7252261	0.94[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs7257857	0.94[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs7259311	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs7508671	0.87[CHB][hapmap]
rs8099940	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs8101089	0.84[JPT][hapmap]
rs8103325	0.94[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs8103459	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs8105629	0.86[CEU][hapmap]
rs8110814	0.83[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs8110967	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs8111189	1.00[CEU][hapmap]
rs8113558	0.86[CEU][hapmap]
rs924485	0.81[JPT][hapmap]
rs924487	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv911417	chr19:21388995-21564001	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv963023	chr19:21491992-21570395	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	esv1793996	chr19:21544242-21609607	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv1801985	chr19:21544242-21609607	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	esv1844586	chr19:21544242-21609607	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs7249636	ZNF429	cis	parietal	SCAN
rs7249636	CTD-2561J22.5	cis	Esophagus Muscularis	GTEx
rs7249636	LOC115648	cis	multi-tissue	Pritchard
rs7249636	ZNF493	cis	Lymphoblastoid	GTEx
rs7249636	ZNF429	cis	Artery Tibial	GTEx
rs7249636	ZNF100	cis	cerebellum	SCAN
rs7249636	ZNF429	cis	cerebellum	SCAN
rs7249636	ZNF429	cis	multi-tissue	Pritchard
rs7249636	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs7249636	ZNF738	cis	parietal	SCAN
rs7249636	CTD-2561J22.5	cis	Thyroid	GTEx
rs7249636	ZNF429	cis	Whole Blood	GTEx
rs7249636	ZNF90	cis	cerebellum	SCAN
rs7249636	ZNF738	cis	cerebellum	SCAN
rs7249636	ZNF493	cis	cerebellum	SCAN
rs7249636	ZNF429	cis	Adipose Subcutaneous	GTEx
rs7249636	ZNF493	cis	multi-tissue	Pritchard

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21542400-21557800	Weak transcription	Gastric	stomach
2	chr19:21542400-21562200	Weak transcription	Colon Smooth Muscle	Colon
3	chr19:21542400-21562200	Weak transcription	Fetal Heart	heart
4	chr19:21542400-21563200	Weak transcription	Brain Substantia Nigra	brain
5	chr19:21542600-21561400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr19:21542600-21561400	Weak transcription	Pancreas	Pancrea
7	chr19:21542800-21561400	Weak transcription	Right Ventricle	heart
8	chr19:21543000-21563000	Weak transcription	NHLF	lung
9	chr19:21543000-21566600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:21543000-21566800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:21543200-21557000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr19:21543400-21560000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
13	chr19:21543400-21560400	ZNF genes & repeats	Fetal Brain Female	brain
14	chr19:21543400-21566400	ZNF genes & repeats	Brain Germinal Matrix	brain
15	chr19:21543400-21570600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
16	chr19:21543600-21563200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr19:21543600-21566400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:21543800-21556800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr19:21543800-21566600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:21543800-21567400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr19:21544200-21560400	ZNF genes & repeats	Primary B cells from cord blood	blood
22	chr19:21544200-21561400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:21544200-21567400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr19:21544200-21567600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:21547400-21567600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
26	chr19:21547800-21557000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
27	chr19:21547800-21571000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr19:21549000-21560600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:21549800-21560400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
30	chr19:21550200-21559200	Strong transcription	Ovary	ovary
31	chr19:21550800-21562200	Weak transcription	Brain Angular Gyrus	brain
32	chr19:21551000-21570800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr19:21551600-21561800	ZNF genes & repeats	Primary T cells from cord blood	blood
34	chr19:21552000-21560400	Strong transcription	Fetal Lung	lung
35	chr19:21552000-21563200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
36	chr19:21552000-21570800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
37	chr19:21552200-21560200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr19:21552200-21561400	Weak transcription	Esophagus	oesophagus
39	chr19:21552400-21559400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:21552800-21559200	Weak transcription	Lung	lung
41	chr19:21552800-21561400	Weak transcription	Aorta	Aorta
42	chr19:21553400-21557000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr19:21553600-21557000	ZNF genes & repeats	Thymus	Thymus
44	chr19:21553600-21558000	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr19:21553800-21559200	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr19:21554000-21557000	Strong transcription	Fetal Thymus	thymus
47	chr19:21554000-21558000	Strong transcription	Fetal Intestine Large	intestine
48	chr19:21554200-21557200	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr19:21554200-21559000	Strong transcription	NH-A	brain
50	chr19:21554200-21561600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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