Variant report

Variant	rs3786834
Chromosome Location	chr19:39126466-39126467
allele	G/T
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:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39033468..39036345-chr19:39125493..39127888,3	K562	blood:
2	chr19:39124852..39127091-chr19:39168674..39171313,2	K562	blood:
3	chr19:39125520..39127850-chr19:39138032..39139918,2	K562	blood:
4	chr19:39107787..39109799-chr19:39125420..39127051,2	MCF-7	breast:
5	chr19:39118492..39120999-chr19:39123202..39126576,3	MCF-7	breast:
6	chr19:39033384..39036751-chr19:39123967..39127917,4	K562	blood:
7	chr19:39125533..39130601-chr19:39201644..39207054,6	MCF-7	breast:
8	chr19:39126407..39129417-chr19:39138116..39140606,3	MCF-7	breast:
9	chr19:39033772..39036275-chr19:39124908..39126988,2	MCF-7	breast:
10	chr19:39126238..39128898-chr19:39190173..39192471,2	K562	blood:
11	chr19:39113554..39117374-chr19:39123915..39127746,4	MCF-7	breast:
12	chr19:39125934..39129387-chr19:39129539..39132887,4	MCF-7	breast:
13	chr19:39126429..39128678-chr19:39138239..39140432,2	K562	blood:
14	chr19:39106811..39110494-chr19:39123822..39128125,5	K562	blood:
15	chr19:39126147..39129376-chr19:39327269..39331362,4	MCF-7	breast:
16	chr19:39126170..39130709-chr19:39210922..39213805,4	MCF-7	breast:
17	chr19:39125626..39127336-chr19:39202058..39204269,2	K562	blood:
18	chr19:38892716..38897062-chr19:39125285..39127901,4	K562	blood:
19	chr19:39112082..39114534-chr19:39125989..39129017,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000178982	Chromatin interaction
ENSG00000104814	Chromatin interaction
ENSG00000130244	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10445564	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12976749	0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12977469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13345885	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1862371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1978443	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2232992	0.87[CEU][hapmap]
rs2287732	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2287733	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4592774	0.80[EUR][1000 genomes]
rs62120358	0.88[EUR][1000 genomes]
rs7251456	0.81[CEU][hapmap]
rs750438	0.94[CEU][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs888994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9304576	0.81[CHB][hapmap]

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	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	nsv911667	chr19:39119898-39143289	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39111000-39127000	Strong transcription	Thymus	Thymus
2	chr19:39111000-39127400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr19:39111000-39128800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr19:39111200-39126600	Strong transcription	Sigmoid Colon	Sigmoid Colon
5	chr19:39111200-39127600	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr19:39111200-39127600	Strong transcription	Brain Anterior Caudate	brain
7	chr19:39111200-39130400	Strong transcription	Stomach Smooth Muscle	stomach
8	chr19:39111200-39130800	Strong transcription	Fetal Stomach	stomach
9	chr19:39111200-39131000	Weak transcription	Right Atrium	heart
10	chr19:39111800-39127200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr19:39114400-39126600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:39115600-39127200	Weak transcription	NHDF-Ad	bronchial
13	chr19:39120600-39127400	Weak transcription	NH-A	brain
14	chr19:39120800-39137800	Weak transcription	Fetal Brain Male	brain
15	chr19:39121600-39132400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr19:39123000-39127400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr19:39123800-39127200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr19:39123800-39132600	Weak transcription	Gastric	stomach
19	chr19:39123800-39137800	Weak transcription	Ovary	ovary
20	chr19:39125200-39127000	Genic enhancers	Primary T cells fromperipheralblood	blood
21	chr19:39125200-39127000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr19:39125200-39127000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr19:39125200-39127600	Genic enhancers	GM12878-XiMat	blood
24	chr19:39125200-39127800	Genic enhancers	A549	lung
25	chr19:39125200-39128000	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr19:39125200-39128200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr19:39125400-39126800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
28	chr19:39125400-39126800	Genic enhancers	Esophagus	oesophagus
29	chr19:39125400-39126800	Genic enhancers	HMEC	breast
30	chr19:39125400-39127200	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr19:39125400-39127200	Genic enhancers	Fetal Intestine Large	intestine
32	chr19:39125400-39127400	Genic enhancers	Primary B cells from peripheral blood	blood
33	chr19:39125400-39127400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr19:39125400-39127600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr19:39125400-39127800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
36	chr19:39125400-39127800	Genic enhancers	Left Ventricle	heart
37	chr19:39125400-39128000	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr19:39125400-39128000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr19:39125400-39128000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr19:39125400-39128000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr19:39125400-39128000	Genic enhancers	Fetal Muscle Trunk	muscle
42	chr19:39125400-39128000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
43	chr19:39125400-39128400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr19:39125400-39128400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:39125400-39128400	Genic enhancers	Fetal Intestine Small	intestine
46	chr19:39125400-39128400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
47	chr19:39125400-39128400	Genic enhancers	NHEK	skin
48	chr19:39125400-39128800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr19:39125400-39129600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr19:39125600-39126600	Genic enhancers	Lung	lung

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