Variant report

Variant	rs10415646
Chromosome Location	chr19:39180458-39180459
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	chr19:39174872..39176720-chr19:39177328..39180654,3	K562	blood:
2	chr19:39176509..39181573-chr19:39186750..39192510,7	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10403540	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10406778	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10415219	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10421560	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083475	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12460849	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12462270	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13343794	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16972767	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2279144	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2303040	0.82[EUR][1000 genomes]
rs28488032	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28624276	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3745859	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3786835	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3786837	0.87[EUR][1000 genomes]
rs3786839	0.97[EUR][1000 genomes]
rs3786845	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3786848	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3786851	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3810341	0.83[ASN][1000 genomes]
rs55876653	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55945853	0.85[EUR][1000 genomes]
rs56113315	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56365761	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62120083	0.84[EUR][1000 genomes]
rs62121814	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62121816	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62121818	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7251903	0.98[EUR][1000 genomes]
rs7252589	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7254100	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8107416	0.80[EUR][1000 genomes]
rs8111746	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs883394	0.96[EUR][1000 genomes]
rs883433	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs979971	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs979972	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	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
5	nsv817834	chr19:39174332-39237950	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	esv1826260	chr19:39178364-39248836	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS 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 target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39164400-39200200	Genic enhancers	Fetal Intestine Small	intestine
2	chr19:39164800-39183800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:39167400-39180800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:39169200-39181000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr19:39170000-39183400	Enhancers	Placenta	Placenta
6	chr19:39174800-39182800	Weak transcription	Dnd41	blood
7	chr19:39175000-39181000	Weak transcription	Aorta	Aorta
8	chr19:39175000-39181200	Enhancers	Fetal Heart	heart
9	chr19:39175600-39182800	Genic enhancers	NHEK	skin
10	chr19:39176400-39182600	Weak transcription	Ovary	ovary
11	chr19:39176800-39182000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr19:39176800-39182000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr19:39176800-39182800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr19:39177000-39183000	Weak transcription	Fetal Brain Female	brain
15	chr19:39177200-39180800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr19:39177200-39182400	Weak transcription	Brain Angular Gyrus	brain
17	chr19:39177200-39182600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:39177200-39195000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr19:39177400-39180600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr19:39177400-39180800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:39177400-39180800	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr19:39177400-39180800	Enhancers	HMEC	breast
23	chr19:39177400-39181600	Weak transcription	Brain Anterior Caudate	brain
24	chr19:39177400-39181600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr19:39177400-39181600	Weak transcription	Brain Substantia Nigra	brain
26	chr19:39177400-39182200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr19:39177400-39182400	Weak transcription	Fetal Lung	lung
28	chr19:39177400-39182400	Weak transcription	Gastric	stomach
29	chr19:39177400-39182600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr19:39177400-39182600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr19:39177400-39183400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr19:39177600-39180600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr19:39177600-39180800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr19:39177600-39181000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr19:39177600-39182400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr19:39177600-39182600	Weak transcription	Colonic Mucosa	Colon
37	chr19:39177600-39182800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr19:39177600-39182800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr19:39177600-39182800	Weak transcription	Primary T cells from cord blood	blood
40	chr19:39177800-39182800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr19:39178000-39180800	Weak transcription	Small Intestine	intestine
42	chr19:39178000-39182400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr19:39178000-39182600	Weak transcription	Fetal Thymus	thymus
44	chr19:39178000-39183600	Genic enhancers	Muscle Satellite Cultured Cells	--
45	chr19:39178200-39181000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr19:39178200-39181000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr19:39178200-39181000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr19:39178200-39181200	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr19:39178400-39180800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr19:39178600-39182400	Weak transcription	Stomach Mucosa	stomach

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