Variant report

Variant	rs10403540
Chromosome Location	chr19:39204846-39204847
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39136969..39142530-chr19:39203025..39206877,12	MCF-7	breast:
2	chr19:39151900..39153408-chr19:39203433..39205156,2	MCF-7	breast:
3	chr19:39125533..39130601-chr19:39201644..39207054,6	MCF-7	breast:
4	chr19:39204751..39205762-chr19:39222193..39223010,6	MCF-7	breast:
5	chr19:39204308..39206712-chr19:39213825..39215554,2	MCF-7	breast:
6	chr19:39173836..39175126-chr19:39204742..39205750,26	MCF-7	breast:
7	chr19:39173858..39174895-chr19:39204828..39205582,8	MCF-7	breast:
8	chr19:39154055..39157137-chr19:39203619..39206563,4	MCF-7	breast:
9	chr19:39177569..39179808-chr19:39201559..39205279,5	MCF-7	breast:
10	chr19:39198080..39199648-chr19:39203544..39206243,2	K562	blood:
11	chr19:39173836..39175021-chr19:39204742..39205755,40	MCF-7	breast:
12	chr19:39204563..39206681-chr19:39225565..39227778,2	MCF-7	breast:
13	chr19:38811920..38812880-chr19:39204762..39205833,7	MCF-7	breast:
14	chr19:38811920..38812880-chr19:39204810..39205833,6	MCF-7	breast:
15	chr19:39202818..39205555-chr19:39206868..39209450,2	K562	blood:
16	chr19:39204751..39205762-chr19:39222154..39222900,6	MCF-7	breast:
17	chr19:39173657..39176403-chr19:39201609..39205956,8	MCF-7	breast:
18	chr19:39171849..39173429-chr19:39204483..39206765,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000130402	Chromatin interaction
ENSG00000182472	Chromatin interaction

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

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

rs_ID	r²[population]
rs10406778	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10415219	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10415646	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10421560	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10426809	0.94[JPT][hapmap];1.00[YRI][hapmap]
rs11083475	0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12460849	0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs12462270	1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13343794	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16972767	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2279144	0.95[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28488032	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28624276	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3745859	0.95[CHB][hapmap];0.80[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3786835	0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3786837	0.84[EUR][1000 genomes]
rs3786839	0.94[EUR][1000 genomes]
rs3786845	0.95[CHB][hapmap];0.80[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3786848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3786851	0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3810341	0.86[ASN][1000 genomes]
rs55876653	0.85[ASN][1000 genomes]
rs55945853	0.87[EUR][1000 genomes]
rs56113315	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56365761	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62120083	0.87[EUR][1000 genomes]
rs62121814	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62121816	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62121818	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7251903	0.96[EUR][1000 genomes]
rs7252589	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7254100	0.88[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8107416	0.83[EUR][1000 genomes]
rs8111746	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs883394	0.99[EUR][1000 genomes]
rs883433	0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs979971	0.90[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs979972	0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes];0.85[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	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
2	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
3	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
4	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
5	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
6	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
7	nsv911669	chr19:39196745-39231548	Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39179600-39205800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr19:39182200-39214200	Genic enhancers	Fetal Muscle Trunk	muscle
3	chr19:39182200-39225200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:39184800-39205800	Genic enhancers	A549	lung
5	chr19:39185200-39205800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr19:39186400-39213400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr19:39187200-39205800	Genic enhancers	Right Ventricle	heart
8	chr19:39189400-39223400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr19:39189800-39222800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr19:39190000-39205800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:39190000-39208800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr19:39190000-39218400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr19:39190200-39222600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr19:39190200-39222800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr19:39190400-39206000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
16	chr19:39190400-39208400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr19:39190400-39209200	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr19:39190400-39212000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:39190400-39212200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:39190400-39217000	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr19:39190400-39218000	Strong transcription	Primary T cells from cord blood	blood
22	chr19:39190400-39222400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr19:39190400-39222600	Strong transcription	Dnd41	blood
24	chr19:39190600-39205400	Genic enhancers	Spleen	Spleen
25	chr19:39190600-39205600	Strong transcription	Fetal Brain Female	brain
26	chr19:39190600-39209000	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr19:39190600-39209200	Strong transcription	Placenta Amnion	Placenta Amnion
28	chr19:39190600-39216400	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr19:39190600-39217000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr19:39190600-39219600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr19:39190600-39222800	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr19:39190800-39220400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr19:39190800-39222600	Strong transcription	Primary B cells from peripheral blood	blood
34	chr19:39190800-39222600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr19:39190800-39222800	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr19:39190800-39223000	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr19:39190800-39223000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr19:39191000-39205800	Genic enhancers	Left Ventricle	heart
39	chr19:39191000-39222400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr19:39191000-39222600	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr19:39191400-39205800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr19:39191400-39209400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr19:39191400-39218800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
44	chr19:39192400-39221200	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr19:39192800-39209600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:39193000-39206000	Strong transcription	Primary B cells from cord blood	blood
47	chr19:39193400-39210200	Strong transcription	Brain Germinal Matrix	brain
48	chr19:39195000-39206000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:39195400-39205000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:39195600-39205400	Genic enhancers	Adipose Nuclei	Adipose

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