Variant report

Variant	rs273504
Chromosome Location	chr19:18215247-18215248
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18215138..18216766-chr19:18223836..18225347,2	MCF-7	breast:
2	chr19:18207064..18208834-chr19:18213992..18216646,2	MCF-7	breast:
3	chr19:18213855..18215840-chr19:18226802..18229759,2	K562	blood:
4	chr19:18214304..18215890-chr19:18263415..18265130,2	K562	blood:
5	chr19:18214257..18217360-chr19:18228399..18230348,3	MCF-7	breast:
6	chr19:18201667..18204008-chr19:18212882..18215554,2	MCF-7	breast:
7	chr19:18185895..18188337-chr19:18214059..18216560,2	K562	blood:
8	chr19:18208517..18210174-chr19:18213137..18216099,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000096996	Chromatin interaction
ENSG00000099308	Chromatin interaction
ENSG00000268173	Chromatin interaction
ENSG00000105647	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11086089	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11665905	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667917	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11670228	0.93[EUR][1000 genomes]
rs11672366	0.85[EUR][1000 genomes]
rs11673702	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs273496	0.92[CEU][hapmap]
rs273503	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs273505	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs273506	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs273508	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs273512	0.83[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs4808746	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56971820	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58049250	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62121155	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62121158	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62123561	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7249862	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs740688	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055932	chr19:17923918-18369944	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv543923	chr19:17923918-18369944	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats 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	109 gene(s)	inside rSNPs	diseases
3	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
4	nsv470130	chr19:18047283-18234587	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	esv1837595	chr19:18085428-18393682	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
6	nsv833773	chr19:18152971-18302988	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv911241	chr19:18193191-18304700	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv911242	chr19:18201757-18304700	Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv911243	chr19:18206681-18283501	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv911244	chr19:18206681-18304700	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv911245	chr19:18206681-18338101	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
12	nsv833774	chr19:18213761-18295329	Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv833775	chr19:18213761-18390074	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
14	esv3340166	chr19:18215101-18215332	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs273504	ANKLE1	cis	cerebellum	SCAN
rs273504	HSH2D	cis	cerebellum	SCAN
rs273504	ZNF714	cis	parietal	SCAN
rs273504	KLHL26	cis	cerebellum	SCAN
rs273504	HAPLN4	cis	cerebellum	SCAN
rs273504	TM6SF2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18210000-18215400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr19:18212400-18215400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:18213600-18216000	Enhancers	Fetal Brain Male	brain
4	chr19:18214200-18216000	Enhancers	Fetal Stomach	stomach
5	chr19:18214400-18216000	Enhancers	Spleen	Spleen
6	chr19:18214800-18215800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:18214800-18215800	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr19:18215000-18215400	Active TSS	H1 Cell Line	embryonic stem cell
9	chr19:18215000-18215400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr19:18215000-18215400	Active TSS	Brain Germinal Matrix	brain
11	chr19:18215000-18215400	Active TSS	Brain Hippocampus Middle	brain
12	chr19:18215000-18215400	Flanking Active TSS	Dnd41	blood
13	chr19:18215000-18215400	Active TSS	HSMM	muscle
14	chr19:18215000-18215600	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr19:18215000-18215600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr19:18215000-18215600	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr19:18215000-18215600	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr19:18215000-18215600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:18215000-18215600	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr19:18215000-18215600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr19:18215000-18215600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:18215000-18215600	Active TSS	Fetal Kidney	kidney
23	chr19:18215000-18215600	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr19:18215000-18215600	Flanking Active TSS	Fetal Thymus	thymus
25	chr19:18215000-18215600	Flanking Active TSS	Ovary	ovary
26	chr19:18215000-18215600	Active TSS	A549	lung
27	chr19:18215000-18215800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr19:18215000-18215800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr19:18215000-18215800	Active TSS	H9 Cell Line	embryonic stem cell
30	chr19:18215000-18215800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:18215000-18215800	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr19:18215000-18215800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:18215000-18215800	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr19:18215000-18215800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr19:18215000-18215800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr19:18215000-18215800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr19:18215000-18215800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr19:18215000-18215800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr19:18215000-18215800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr19:18215000-18215800	Flanking Active TSS	Primary B cells from peripheral blood	blood
41	chr19:18215000-18215800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
42	chr19:18215000-18215800	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr19:18215000-18215800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr19:18215000-18215800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr19:18215000-18215800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr19:18215000-18215800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr19:18215000-18215800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr19:18215000-18215800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr19:18215000-18215800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr19:18215000-18215800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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