Variant report

Variant	rs10420548
Chromosome Location	chr19:22017492-22017493
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	chr19:22015861..22017708-chr19:22019251..22022025,2	MCF-7	breast:
2	chr19:21948377..21950622-chr19:22016631..22019164,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198521	Chromatin interaction
ENSG00000197020	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10410478	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10411895	0.81[EUR][1000 genomes]
rs10413659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10418840	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672034	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435048	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28480566	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112965	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3441368	chr19:21781459-22182822	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3339694	chr19:21781479-22182792	Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1063115	chr19:21782104-22528039	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv458525	chr19:21796943-22019697	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv578969	chr19:21796943-22019697	ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking 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	13 gene(s)	inside rSNPs	diseases
6	nsv911424	chr19:21798441-22471156	Strong transcription Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
7	nsv911425	chr19:21841379-22338142	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv833784	chr19:21902647-22037153	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	9 gene(s)	inside rSNPs	diseases
9	nsv1059079	chr19:21940891-22083420	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv3395280	chr19:21968753-22202288	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv911428	chr19:21986292-22106951	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv911429	chr19:21986292-22110219	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 Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv961194	chr19:21998424-22019912	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
14	nsv911430	chr19:22008229-22106951	ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv1062497	chr19:22013911-22102714	Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv543949	chr19:22013911-22102714	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10420548	RP11-420K14.3	cis	lung	GTEx
rs10420548	ZNF100	cis	Artery Tibial	GTEx
rs10420548	VN1R84P	cis	lung	GTEx
rs10420548	RP11-420K14.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21988600-22018000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:21990800-22017600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
3	chr19:21999800-22018200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:22000800-22018200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr19:22000800-22018200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr19:22001000-22018000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr19:22001000-22018000	Weak transcription	Brain Anterior Caudate	brain
8	chr19:22001000-22018000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr19:22001200-22018200	Weak transcription	Gastric	stomach
10	chr19:22002000-22017800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr19:22002600-22018000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr19:22004000-22017600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
13	chr19:22004000-22017800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:22009000-22018000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:22009200-22018200	Weak transcription	Colon Smooth Muscle	Colon
16	chr19:22009400-22018000	Weak transcription	NH-A	brain
17	chr19:22009400-22018200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr19:22009400-22018200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr19:22009400-22018200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr19:22009600-22017800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr19:22009600-22017800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr19:22009600-22018000	Weak transcription	Colonic Mucosa	Colon
23	chr19:22009600-22018200	Weak transcription	Brain Hippocampus Middle	brain
24	chr19:22009600-22018200	Weak transcription	Pancreas	Pancrea
25	chr19:22009600-22018200	Weak transcription	Spleen	Spleen
26	chr19:22009800-22018000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr19:22009800-22018200	Weak transcription	Ovary	ovary
28	chr19:22010000-22017800	Weak transcription	Fetal Kidney	kidney
29	chr19:22010000-22017800	Weak transcription	Placenta	Placenta
30	chr19:22010000-22018000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr19:22010000-22018000	Weak transcription	Adipose Nuclei	Adipose
32	chr19:22010000-22018200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr19:22010200-22018000	Weak transcription	Osteobl	bone
34	chr19:22010400-22018200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr19:22010600-22018200	Weak transcription	Right Ventricle	heart
36	chr19:22010800-22018000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr19:22011000-22017800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr19:22012000-22017600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr19:22012800-22017800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr19:22012800-22018200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr19:22013000-22017800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr19:22013000-22017800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr19:22013000-22018200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:22013000-22018400	Weak transcription	Aorta	Aorta
45	chr19:22013600-22018000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr19:22014400-22018200	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr19:22014600-22017800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr19:22014600-22018000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr19:22014600-22018000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr19:22014600-22018000	Weak transcription	Psoas Muscle	Psoas

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