Variant report

Variant	rs120960
Chromosome Location	chr19:36276767-36276768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:36248580..36254743-chr19:36274692..36280659,6	K562	blood:
2	chr19:36276618..36278741-chr19:36279963..36282089,2	K562	blood:
3	chr19:36229613..36232154-chr19:36276391..36278714,2	MCF-7	breast:
4	chr19:36272079..36274147-chr19:36275099..36277481,2	MCF-7	breast:
5	chr19:36276281..36278595-chr19:36292091..36294891,2	K562	blood:

Variant related genes	Relation type
ENSG00000004776	Chromatin interaction
ENSG00000004777	Chromatin interaction
ENSG00000250799	Chromatin interaction
ENSG00000126246	Chromatin interaction
ENSG00000167595	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10401695	0.83[MEX][hapmap];0.81[TSI][hapmap]
rs173003	0.82[GIH][hapmap]
rs231236	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2619197	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3746281	1.00[CHB][hapmap];0.91[YRI][hapmap]
rs807484	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs807485	1.00[CEU][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8110675	1.00[CHB][hapmap];0.91[YRI][hapmap]

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	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
3	nsv911631	chr19:36169285-36290977	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv911632	chr19:36174176-36288297	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
5	nsv911633	chr19:36206050-36283847	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
6	nsv911634	chr19:36206050-36290977	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
7	nsv1057830	chr19:36210269-36279794	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
8	nsv543997	chr19:36210269-36279794	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	nsv911635	chr19:36217333-36283847	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv458567	chr19:36221051-36283847	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
11	nsv579423	chr19:36221051-36283847	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
12	nsv911636	chr19:36240960-36290977	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
13	nsv911637	chr19:36261928-36309321	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
14	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs120960	COX6B1	trans	parietal	SCAN
rs120960	COX6B1	trans	cerebellum	SCAN
rs120960	ZBTB32	cis	lung	GTEx
rs120960	COX6B1	cis	Muscle Skeletal	GTEx
rs120960	FBXO27	cis	parietal	SCAN
rs120960	UPK1A	trans	cerebellum	SCAN
rs120960	ZBTB32	cis	Thyroid	GTEx
rs120960	AC002398.13	cis	Thyroid	GTEx
rs120960	ZBTB32	cis	Nerve Tibial	GTEx
rs120960	PHLDB3	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36266800-36281800	Weak transcription	Liver	Liver
2	chr19:36267400-36277600	Weak transcription	Right Atrium	heart
3	chr19:36267400-36277800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr19:36267400-36281600	Weak transcription	Small Intestine	intestine
5	chr19:36267600-36279200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr19:36267800-36278000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr19:36267800-36280600	Weak transcription	HUVEC	blood vessel
8	chr19:36267800-36284200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr19:36268400-36278600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:36268400-36278600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:36268400-36284200	Weak transcription	K562	blood
12	chr19:36268600-36277600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr19:36268600-36279200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr19:36268600-36279400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:36268600-36279600	Strong transcription	Thymus	Thymus
16	chr19:36268600-36281000	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr19:36268600-36281000	Strong transcription	Fetal Stomach	stomach
18	chr19:36268800-36277800	Strong transcription	Fetal Muscle Trunk	muscle
19	chr19:36268800-36278400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr19:36268800-36278600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:36268800-36278800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr19:36268800-36279000	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr19:36268800-36280000	Strong transcription	Fetal Muscle Leg	muscle
24	chr19:36269000-36277800	Strong transcription	Fetal Thymus	thymus
25	chr19:36269000-36278400	Strong transcription	Lung	lung
26	chr19:36269000-36278800	Strong transcription	Brain Hippocampus Middle	brain
27	chr19:36269200-36277200	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr19:36269200-36279200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr19:36269400-36278400	Strong transcription	Spleen	Spleen
30	chr19:36269600-36276800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr19:36270000-36277400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr19:36270000-36278400	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr19:36270200-36278400	Strong transcription	Dnd41	blood
34	chr19:36270400-36278200	Weak transcription	Fetal Brain Male	brain
35	chr19:36271000-36277600	Strong transcription	Aorta	Aorta
36	chr19:36271000-36281200	Strong transcription	Brain Germinal Matrix	brain
37	chr19:36271000-36281200	Strong transcription	Fetal Brain Female	brain
38	chr19:36271400-36277400	Strong transcription	NHLF	lung
39	chr19:36272200-36281000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:36272600-36279600	Weak transcription	Left Ventricle	heart
41	chr19:36272800-36277600	Strong transcription	Gastric	stomach
42	chr19:36273000-36276800	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr19:36273000-36280600	Weak transcription	Colonic Mucosa	Colon
44	chr19:36273000-36282800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:36273200-36277800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr19:36273200-36278000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr19:36273200-36284200	Weak transcription	Osteobl	bone
48	chr19:36273600-36281000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr19:36273600-36281800	Weak transcription	Pancreas	Pancrea
50	chr19:36273600-36283400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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