Variant report

Variant	rs2435049
Chromosome Location	chr19:22016610-22016611
allele	A/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	chr19:22014202..22016734-chr19:22017712..22020102,2	K562	blood:

Variant related genes	Relation type
ENSG00000198521	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10407896	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10414358	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12463314	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12609186	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1877130	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2244127	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2435036	0.87[ASN][1000 genomes]
rs2435039	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2457784	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2457792	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2457794	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2457798	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2457800	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4075276	0.85[ASN][1000 genomes]
rs7247610	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2435049	RP11-420K14.3	cis	Muscle Skeletal	GTEx
rs2435049	ZNF100	Cis_1M	lymphoblastoid	RTeQTL
rs2435049	RP11-420K14.3	cis	Whole Blood	GTEx
rs2435049	ZNF100	cis	Adipose Subcutaneous	GTEx
rs2435049	ZNF100	cis	Nerve Tibial	GTEx
rs2435049	ZNF100	cis	Muscle Skeletal	GTEx
rs2435049	ZNF100	cis	Skin Sun Exposed Lower leg	GTEx
rs2435049	RP11-420K14.3	cis	Esophagus Muscularis	GTEx
rs2435049	RP11-420K14.3	cis	lung	GTEx
rs2435049	ZNF100	cis	Artery Tibial	GTEx

Chromatin state (count:90 , 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	chr19:21988800-22017200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:21990800-22017600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
4	chr19:21999800-22018200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:22000800-22018200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr19:22000800-22018200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr19:22001000-22018000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr19:22001000-22018000	Weak transcription	Brain Anterior Caudate	brain
9	chr19:22001000-22018000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr19:22001200-22018200	Weak transcription	Gastric	stomach
11	chr19:22002000-22017800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr19:22002600-22018000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr19:22004000-22017600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
14	chr19:22004000-22017800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:22009000-22018000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:22009200-22018200	Weak transcription	Colon Smooth Muscle	Colon
17	chr19:22009400-22018000	Weak transcription	NH-A	brain
18	chr19:22009400-22018200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:22009400-22018200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr19:22009400-22018200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr19:22009600-22017800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr19:22009600-22017800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr19:22009600-22018000	Weak transcription	Colonic Mucosa	Colon
24	chr19:22009600-22018200	Weak transcription	Brain Hippocampus Middle	brain
25	chr19:22009600-22018200	Weak transcription	Pancreas	Pancrea
26	chr19:22009600-22018200	Weak transcription	Spleen	Spleen
27	chr19:22009800-22016800	Weak transcription	Left Ventricle	heart
28	chr19:22009800-22018000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr19:22009800-22018200	Weak transcription	Ovary	ovary
30	chr19:22010000-22017000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr19:22010000-22017800	Weak transcription	Fetal Kidney	kidney
32	chr19:22010000-22017800	Weak transcription	Placenta	Placenta
33	chr19:22010000-22018000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr19:22010000-22018000	Weak transcription	Adipose Nuclei	Adipose
35	chr19:22010000-22018200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr19:22010200-22018000	Weak transcription	Osteobl	bone
37	chr19:22010400-22018200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr19:22010600-22018200	Weak transcription	Right Ventricle	heart
39	chr19:22010800-22018000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr19:22011000-22017800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr19:22012000-22017600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr19:22012800-22016800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr19:22012800-22017800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr19:22012800-22018200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr19:22013000-22017800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr19:22013000-22017800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr19:22013000-22018200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr19:22013000-22018400	Weak transcription	Aorta	Aorta
49	chr19:22013600-22018000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr19:22014200-22017400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin

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