Variant report

Variant	rs1227589
Chromosome Location	chr19:37326892-37326893
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37325206..37326948-chr19:37327588..37329435,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197863	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1035441	0.86[CHB][hapmap];0.81[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs11084867	0.86[CHB][hapmap];0.92[YRI][hapmap]
rs1148399	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1227799	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1227804	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1227819	0.86[EUR][1000 genomes]
rs1227820	0.86[EUR][1000 genomes]
rs1673086	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs1726702	0.93[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2462577	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35488109	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs8106752	0.86[CHB][hapmap];0.91[YRI][hapmap]
rs826965	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs826967	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription 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 miRNA target site	25 gene(s)	inside rSNPs	diseases
18	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription 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	25 gene(s)	inside rSNPs	diseases
19	nsv911651	chr19:37300554-37428465	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
20	esv3354270	chr19:37309161-37364929	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
21	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
22	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1227589	IL28B	cis	cerebellum	SCAN
rs1227589	POU2F2	cis	cerebellum	SCAN
rs1227589	ZFP112	cis	parietal	SCAN
rs1227589	SUPT5H	cis	parietal	SCAN
rs1227589	SPINT2	cis	cerebellum	SCAN
rs1227589	ZNF404	cis	parietal	SCAN
rs1227589	PAFAH1B3	cis	cerebellum	SCAN
rs1227589	TIMM50	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37287400-37327400	ZNF genes & repeats	Liver	Liver
2	chr19:37289200-37327000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
3	chr19:37289400-37327600	ZNF genes & repeats	Adipose Nuclei	Adipose
4	chr19:37289600-37327400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:37289600-37327400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
6	chr19:37292000-37328400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
7	chr19:37295000-37327200	ZNF genes & repeats	Fetal Lung	lung
8	chr19:37295600-37327200	ZNF genes & repeats	Fetal Brain Female	brain
9	chr19:37298200-37327000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr19:37298400-37328200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
11	chr19:37299400-37327000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr19:37300000-37327200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
13	chr19:37303200-37327800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
14	chr19:37303200-37327800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
15	chr19:37303200-37328000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr19:37303400-37327000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr19:37303800-37327000	ZNF genes & repeats	Brain Germinal Matrix	brain
18	chr19:37304200-37327400	ZNF genes & repeats	Dnd41	blood
19	chr19:37308400-37327400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr19:37308600-37327200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
21	chr19:37308600-37327600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:37311000-37328200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr19:37312600-37328000	ZNF genes & repeats	Fetal Intestine Small	intestine
24	chr19:37318000-37327200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
25	chr19:37318200-37327000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
26	chr19:37318200-37328200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:37318400-37327200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:37319600-37327000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr19:37321000-37327200	ZNF genes & repeats	Brain Substantia Nigra	brain
30	chr19:37322200-37327000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:37322200-37327400	ZNF genes & repeats	NHEK	skin
32	chr19:37322600-37328200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr19:37323200-37327600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
34	chr19:37323600-37328200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr19:37323600-37328200	Weak transcription	Gastric	stomach
36	chr19:37323600-37328200	Weak transcription	Right Ventricle	heart
37	chr19:37323600-37328200	Weak transcription	HUVEC	blood vessel
38	chr19:37323600-37328600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr19:37323800-37328000	Weak transcription	HSMMtube	muscle
40	chr19:37324800-37327800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
41	chr19:37324800-37328400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr19:37325000-37328200	Weak transcription	Placenta	Placenta
43	chr19:37325200-37328200	Weak transcription	Left Ventricle	heart
44	chr19:37325600-37328000	Weak transcription	Osteobl	bone
45	chr19:37325600-37328200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr19:37325800-37327000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr19:37325800-37328200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr19:37326200-37327800	Weak transcription	Fetal Stomach	stomach
49	chr19:37326400-37327400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:37326400-37327600	ZNF genes & repeats	Rectal Smooth Muscle	rectum

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