Variant report

Variant	rs2017784
Chromosome Location	chr19:39309648-39309649
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10401746	0.88[LWK][hapmap];1.00[YRI][hapmap]
rs2229259	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs8100689	1.00[YRI][hapmap]
rs8100781	1.00[YRI][hapmap]
rs8112471	1.00[YRI][hapmap]
rs862456	0.88[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv911670	chr19:39250308-39322087	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv911672	chr19:39252238-39318006	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2017784	ECH1	Cis_1M	lymphoblastoid	RTeQTL
rs2017784	SNRPD2	cis	cerebellum	SCAN
rs2017784	TTC9B	cis	cerebellum	SCAN
rs2017784	PSG8	cis	parietal	SCAN
rs2017784	CEACAM6	cis	cerebellum	SCAN
rs2017784	ATP1A3	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39284000-39318200	Weak transcription	Fetal Kidney	kidney
2	chr19:39290800-39310600	Weak transcription	HMEC	breast
3	chr19:39294600-39309800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:39294800-39309800	Weak transcription	Psoas Muscle	Psoas
5	chr19:39296200-39318200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr19:39296400-39318000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr19:39296400-39318200	Weak transcription	NHEK	skin
8	chr19:39301400-39320200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr19:39304000-39317600	Weak transcription	HSMMtube	muscle
10	chr19:39304200-39312800	Genic enhancers	Fetal Intestine Small	intestine
11	chr19:39304400-39316800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr19:39304400-39321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr19:39304600-39318200	Weak transcription	Osteobl	bone
14	chr19:39304800-39320800	Weak transcription	HSMM	muscle
15	chr19:39305000-39310000	Strong transcription	Fetal Muscle Leg	muscle
16	chr19:39305000-39315000	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr19:39305200-39311400	Strong transcription	Primary B cells from peripheral blood	blood
18	chr19:39305200-39316000	Strong transcription	Primary T cells from cord blood	blood
19	chr19:39305200-39321600	Strong transcription	Fetal Stomach	stomach
20	chr19:39305400-39309800	Strong transcription	Liver	Liver
21	chr19:39305400-39315800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr19:39305400-39321000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr19:39305600-39309800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr19:39305600-39309800	Strong transcription	Spleen	Spleen
25	chr19:39305600-39310200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr19:39305600-39310400	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr19:39305600-39312200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr19:39305600-39314000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:39305600-39314000	Strong transcription	Esophagus	oesophagus
30	chr19:39305600-39314000	Strong transcription	Lung	lung
31	chr19:39305600-39314400	Strong transcription	Thymus	Thymus
32	chr19:39305600-39318800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr19:39305600-39320400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr19:39305600-39321000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr19:39305800-39309800	Strong transcription	Adipose Nuclei	Adipose
36	chr19:39305800-39309800	Genic enhancers	Fetal Intestine Large	intestine
37	chr19:39305800-39310200	Strong transcription	Aorta	Aorta
38	chr19:39305800-39310400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
39	chr19:39305800-39310400	Strong transcription	Stomach Smooth Muscle	stomach
40	chr19:39305800-39310400	Strong transcription	Dnd41	blood
41	chr19:39305800-39311400	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr19:39305800-39312000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr19:39305800-39312200	Strong transcription	Brain Cingulate Gyrus	brain
44	chr19:39305800-39312600	Strong transcription	Fetal Brain Female	brain
45	chr19:39305800-39312800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr19:39305800-39313400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr19:39306000-39310000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr19:39306000-39310200	Strong transcription	Brain Anterior Caudate	brain
49	chr19:39306000-39312000	Strong transcription	Colon Smooth Muscle	Colon
50	chr19:39306400-39317800	Weak transcription	Small Intestine	intestine

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