Variant report

Variant	rs10406778
Chromosome Location	chr19:39170473-39170474
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39169983..39173495-chr19:39173704..39177059,4	K562	blood:
2	chr19:39169995..39171948-chr19:39172735..39174419,2	MCF-7	breast:
3	chr19:39138054..39139945-chr19:39169569..39171222,2	K562	blood:
4	chr19:39165775..39169288-chr19:39170285..39176842,12	K562	blood:
5	chr19:39140553..39142565-chr19:39169330..39171049,2	MCF-7	breast:
6	chr19:39124852..39127091-chr19:39168674..39171313,2	K562	blood:

Variant related genes	Relation type
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10403540	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10404257	0.80[ASN][1000 genomes]
rs10415219	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10415646	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10421560	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11083475	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12460849	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12462270	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13343794	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16972767	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2279144	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2303040	0.84[EUR][1000 genomes]
rs28488032	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28624276	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3745859	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3786835	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3786837	0.92[EUR][1000 genomes]
rs3786839	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3786845	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3786848	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3786851	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3810341	0.87[ASN][1000 genomes]
rs55876653	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55945853	0.83[EUR][1000 genomes]
rs56113315	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56365761	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62120083	0.82[EUR][1000 genomes]
rs62121814	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62121816	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62121818	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251903	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7252589	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254100	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8111746	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs883394	0.91[EUR][1000 genomes]
rs883433	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs979971	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs979972	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39160400-39173400	Weak transcription	Brain Germinal Matrix	brain
2	chr19:39161200-39176000	Weak transcription	Fetal Brain Male	brain
3	chr19:39161200-39176000	Weak transcription	Fetal Brain Female	brain
4	chr19:39162200-39173400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:39162400-39172000	Enhancers	Left Ventricle	heart
6	chr19:39162800-39173200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:39164400-39172600	Enhancers	Small Intestine	intestine
8	chr19:39164400-39200200	Genic enhancers	Fetal Intestine Small	intestine
9	chr19:39164600-39170800	Genic enhancers	Osteobl	bone
10	chr19:39164600-39173800	Genic enhancers	HepG2	liver
11	chr19:39164600-39178200	Enhancers	Primary T cells fromperipheralblood	blood
12	chr19:39164800-39170600	Enhancers	Primary B cells from peripheral blood	blood
13	chr19:39164800-39170800	Enhancers	Brain Hippocampus Middle	brain
14	chr19:39164800-39170800	Enhancers	Psoas Muscle	Psoas
15	chr19:39164800-39171000	Genic enhancers	Rectal Mucosa Donor 31	rectum
16	chr19:39164800-39171400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:39164800-39172600	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr19:39164800-39173800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr19:39164800-39177600	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr19:39164800-39179200	Enhancers	Pancreas	Pancrea
21	chr19:39164800-39179800	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr19:39164800-39183800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr19:39165000-39174200	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr19:39165200-39171800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:39165400-39172000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
26	chr19:39165400-39172600	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr19:39165400-39178200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:39165600-39171200	Enhancers	GM12878-XiMat	blood
29	chr19:39165600-39172000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr19:39165600-39174000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr19:39166000-39178200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr19:39166200-39172400	Genic enhancers	NHEK	skin
33	chr19:39166200-39173800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr19:39166200-39173800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr19:39166400-39173800	Genic enhancers	HMEC	breast
36	chr19:39166600-39171200	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr19:39166600-39173400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:39167200-39171800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr19:39167200-39173600	Enhancers	Stomach Mucosa	stomach
40	chr19:39167200-39173800	Genic enhancers	Fetal Intestine Large	intestine
41	chr19:39167200-39175600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr19:39167400-39173600	Genic enhancers	Lung	lung
43	chr19:39167400-39173800	Genic enhancers	NHLF	lung
44	chr19:39167400-39174400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr19:39167400-39180800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr19:39167600-39170600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
47	chr19:39167600-39170800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr19:39167600-39173400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr19:39167600-39173800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:39167600-39174000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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