Variant report

Variant	rs321946
Chromosome Location	chr19:52859828-52859829
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	chr19:52839457..52840970-chr19:52859823..52861892,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167554	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs172804	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2657935	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs321941	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs321942	0.88[JPT][hapmap];0.84[AFR][1000 genomes]
rs321943	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs321945	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs321947	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs321949	0.81[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv458742	chr19:52808986-52866171	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
8	nsv580008	chr19:52808986-52866171	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
9	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv912302	chr19:52859828-52928039	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs321946	LILRB2	cis	cerebellum	SCAN
rs321946	TNNT1	cis	cerebellum	SCAN
rs321946	ZBTB45	cis	cerebellum	SCAN
rs321946	ZNF582	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52840400-52865400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr19:52840600-52861200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:52847200-52860000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:52848000-52862600	Weak transcription	Fetal Heart	heart
5	chr19:52848400-52870400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:52849600-52861400	ZNF genes & repeats	Fetal Intestine Small	intestine
7	chr19:52849800-52872200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:52850400-52862000	Strong transcription	Fetal Brain Female	brain
9	chr19:52850800-52860600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr19:52850800-52861200	Strong transcription	Stomach Smooth Muscle	stomach
11	chr19:52850800-52870200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
12	chr19:52850800-52870200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:52851600-52864200	Strong transcription	Brain Germinal Matrix	brain
14	chr19:52854200-52860400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr19:52854600-52861200	Strong transcription	Fetal Muscle Leg	muscle
16	chr19:52855200-52860600	Strong transcription	Fetal Stomach	stomach
17	chr19:52855800-52860400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
18	chr19:52856400-52861400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr19:52856600-52860600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr19:52856600-52864200	ZNF genes & repeats	Liver	Liver
21	chr19:52856800-52860400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:52856800-52860400	Strong transcription	Left Ventricle	heart
23	chr19:52856800-52860600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr19:52856800-52861000	Strong transcription	Fetal Lung	lung
25	chr19:52856800-52870200	ZNF genes & repeats	Ovary	ovary
26	chr19:52857000-52860200	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr19:52857000-52860200	Strong transcription	Fetal Intestine Large	intestine
28	chr19:52857000-52860400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr19:52857000-52860400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
30	chr19:52857000-52860400	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr19:52857000-52860600	ZNF genes & repeats	Primary B cells from cord blood	blood
32	chr19:52857000-52860600	ZNF genes & repeats	Lung	lung
33	chr19:52857000-52860800	Strong transcription	Brain Anterior Caudate	brain
34	chr19:52857000-52861000	Strong transcription	Fetal Muscle Trunk	muscle
35	chr19:52857200-52860200	Strong transcription	Brain Angular Gyrus	brain
36	chr19:52857200-52860400	Strong transcription	HSMMtube	muscle
37	chr19:52857200-52860600	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr19:52857200-52861200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
39	chr19:52857400-52860400	ZNF genes & repeats	Primary T cells from cord blood	blood
40	chr19:52857600-52861200	ZNF genes & repeats	Aorta	Aorta
41	chr19:52857600-52865200	Strong transcription	Brain Hippocampus Middle	brain
42	chr19:52857800-52860400	Strong transcription	Brain Cingulate Gyrus	brain
43	chr19:52858000-52860600	ZNF genes & repeats	Thymus	Thymus
44	chr19:52858000-52862000	Strong transcription	Fetal Kidney	kidney
45	chr19:52858200-52860400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
46	chr19:52858200-52860400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
47	chr19:52858200-52860400	ZNF genes & repeats	Adipose Nuclei	Adipose
48	chr19:52858200-52860600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
49	chr19:52858200-52860600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr19:52858200-52861600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived

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