Variant report

Variant	rs1227800
Chromosome Location	chr19:37289449-37289450
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37287538..37289947-chr19:37340425..37342708,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251247	Chromatin interaction
ENSG00000197863	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10410980	0.94[EUR][1000 genomes]
rs10420413	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1148384	0.85[ASN][1000 genomes]
rs1148387	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1148400	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1148401	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1227560	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1227796	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1227797	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1227802	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1227803	0.85[ASN][1000 genomes]
rs1227805	0.85[ASN][1000 genomes]
rs1227806	0.85[ASN][1000 genomes]
rs1227809	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1227824	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1227826	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1227863	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1227864	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1227865	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1227867	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12982205	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1302670	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1726703	0.86[ASN][1000 genomes]
rs1726717	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2445877	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2445878	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2695086	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28372636	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35967992	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3745775	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4806353	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4806365	0.83[EUR][1000 genomes]
rs542847	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57193089	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62114321	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62114322	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8106994	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers 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 miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription 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 miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv469794	chr19:37129858-37310257	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv482392	chr19:37129858-37310257	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	esv34384	chr19:37134068-37330613	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv817833	chr19:37146694-37357289	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription 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 miRNA target site	33 gene(s)	inside rSNPs	diseases
10	esv3517005	chr19:37193712-37364110	Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	esv3517004	chr19:37193762-37363960	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
12	esv3517006	chr19:37193762-37363960	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
13	nsv911650	chr19:37241141-37331614	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
14	nsv521605	chr19:37261810-37483444	ZNF genes & repeats Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv963042	chr19:37271305-37296858	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
16	nsv1060155	chr19:37274915-37458788	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS 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	14 gene(s)	inside rSNPs	diseases
17	nsv544000	chr19:37274915-37458788	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
19	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers 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 miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1227800	LOC284408	cis	brain	BrainEAC

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37287400-37289600	Active TSS	Primary T helper cells PMA-I stimulated	--
2	chr19:37287400-37289600	Active TSS	Brain Anterior Caudate	brain
3	chr19:37287400-37289800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr19:37287400-37290000	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr19:37287400-37327400	ZNF genes & repeats	Liver	Liver
6	chr19:37287600-37289600	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr19:37287600-37289800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr19:37287600-37289800	Active TSS	Duodenum Mucosa	Duodenum
9	chr19:37287600-37289800	Active TSS	NHLF	lung
10	chr19:37287600-37290000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr19:37287600-37290000	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr19:37287600-37290200	Active TSS	Colon Smooth Muscle	Colon
13	chr19:37287600-37290200	ZNF genes & repeats	Fetal Brain Male	brain
14	chr19:37287600-37290200	ZNF genes & repeats	A549	lung
15	chr19:37287600-37291000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
16	chr19:37287800-37289600	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr19:37287800-37289600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:37287800-37289800	Active TSS	NHDF-Ad	bronchial
19	chr19:37287800-37290200	ZNF genes & repeats	GM12878-XiMat	blood
20	chr19:37287800-37294800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr19:37288000-37289600	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr19:37288000-37289600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
23	chr19:37288000-37290000	Active TSS	Fetal Heart	heart
24	chr19:37288600-37289600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:37288600-37289600	Active TSS	Dnd41	blood
26	chr19:37289000-37289600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr19:37289000-37289600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr19:37289000-37289600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:37289000-37289600	Enhancers	Fetal Muscle Trunk	muscle
30	chr19:37289000-37289600	Weak transcription	Psoas Muscle	Psoas
31	chr19:37289000-37289800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:37289000-37289800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:37289000-37289800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr19:37289000-37289800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr19:37289000-37290200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr19:37289000-37290200	Weak transcription	Stomach Mucosa	stomach
37	chr19:37289000-37290600	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr19:37289000-37290800	Weak transcription	Brain Substantia Nigra	brain
39	chr19:37289000-37292600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:37289000-37293600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:37289000-37293600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr19:37289000-37295000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
43	chr19:37289000-37296400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr19:37289000-37309200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr19:37289200-37289600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr19:37289200-37289600	Active TSS	Primary T cells from cord blood	blood
47	chr19:37289200-37289600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr19:37289200-37289600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr19:37289200-37289600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr19:37289200-37289600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum

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