Variant report

Variant	rs11666561
Chromosome Location	chr19:53397248-53397249
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	chr18:61637223..61637841-chr19:53397208..53398194,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000166401	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10410884	0.84[CEU][hapmap]
rs11666550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668258	0.82[EUR][1000 genomes]
rs11670640	0.82[EUR][1000 genomes]
rs11670858	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670922	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671330	0.82[EUR][1000 genomes]
rs13345475	0.84[CEU][hapmap]
rs8110526	0.90[CEU][hapmap]
rs8111265	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912306	chr19:53092465-53400760	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv912307	chr19:53092465-53433054	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv912308	chr19:53092465-53436337	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv912309	chr19:53092465-53440653	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS 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	32 gene(s)	inside rSNPs	diseases
5	nsv912310	chr19:53092465-53451291	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv912313	chr19:53103875-53436337	ZNF genes & repeats Weak transcription Strong transcription Active TSS 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	30 gene(s)	inside rSNPs	diseases
7	nsv912317	chr19:53105547-53440653	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv1066762	chr19:53112568-53552217	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
9	nsv912318	chr19:53118278-53451291	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer 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
10	nsv432072	chr19:53144788-53554388	Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	esv3401212	chr19:53151131-53482063	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv912321	chr19:53186836-53451291	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
13	nsv1058903	chr19:53193570-53489633	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
14	nsv1067280	chr19:53193570-53567287	Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
15	nsv544062	chr19:53193570-53567287	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer 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	33 gene(s)	inside rSNPs	diseases
16	nsv580030	chr19:53194344-53547394	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
17	nsv1057118	chr19:53195426-53480449	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
18	nsv530807	chr19:53210488-53695881	Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers 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	43 gene(s)	inside rSNPs	diseases
19	nsv912323	chr19:53249347-53451291	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription 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	20 gene(s)	inside rSNPs	diseases
20	esv3431689	chr19:53291230-53483998	Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
21	nsv458747	chr19:53302481-53424324	ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
22	nsv580034	chr19:53302481-53424324	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
23	nsv912329	chr19:53317001-53440653	Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
24	nsv912330	chr19:53317001-53478109	Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers 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	18 gene(s)	inside rSNPs	diseases
25	nsv1064234	chr19:53346827-53480449	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
26	esv3319159	chr19:53361167-53446431	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
27	esv3319160	chr19:53361308-53446343	ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
28	nsv912340	chr19:53370345-53430362	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Strong transcription 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	11 gene(s)	inside rSNPs	diseases
29	esv3326632	chr19:53371248-53697569	Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
30	nsv580045	chr19:53374787-53401760	Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
31	esv3392897	chr19:53389142-53418469	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11666561	ZNF71	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53380400-53398800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:53381800-53397400	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr19:53381800-53398200	Strong transcription	Dnd41	blood
4	chr19:53384000-53397600	Strong transcription	Fetal Muscle Trunk	muscle
5	chr19:53385200-53399400	Weak transcription	Psoas Muscle	Psoas
6	chr19:53385400-53399400	Weak transcription	Fetal Heart	heart
7	chr19:53385600-53399000	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr19:53385600-53399800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr19:53386200-53399000	Strong transcription	Fetal Stomach	stomach
10	chr19:53387000-53399000	Strong transcription	Fetal Muscle Leg	muscle
11	chr19:53387000-53399800	Weak transcription	Fetal Brain Male	brain
12	chr19:53387200-53399800	Weak transcription	NHLF	lung
13	chr19:53387400-53398600	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr19:53388200-53399400	Weak transcription	Hela-S3	cervix
15	chr19:53388200-53399800	Weak transcription	HUVEC	blood vessel
16	chr19:53388400-53399000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr19:53388400-53399800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr19:53388600-53397400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:53388600-53398400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:53388600-53399200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:53388800-53399000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr19:53389200-53398600	Strong transcription	Fetal Intestine Large	intestine
23	chr19:53389200-53399000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:53390000-53399000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr19:53390000-53399800	Weak transcription	Stomach Mucosa	stomach
26	chr19:53390200-53399800	Weak transcription	Small Intestine	intestine
27	chr19:53390400-53399000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr19:53390400-53399800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr19:53391000-53399800	Weak transcription	NHEK	skin
30	chr19:53391200-53399800	Weak transcription	Brain Angular Gyrus	brain
31	chr19:53391200-53399800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr19:53391200-53399800	Weak transcription	Fetal Kidney	kidney
33	chr19:53391200-53400000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr19:53391200-53400000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr19:53391400-53399800	Weak transcription	Right Ventricle	heart
36	chr19:53391400-53399800	Weak transcription	NH-A	brain
37	chr19:53392800-53397400	Strong transcription	Primary T cells from cord blood	blood
38	chr19:53392800-53399800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:53393000-53397600	Strong transcription	Thymus	Thymus
40	chr19:53393200-53399800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr19:53393200-53399800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr19:53393400-53399800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr19:53393400-53399800	Weak transcription	NHDF-Ad	bronchial
44	chr19:53393600-53399800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr19:53393600-53400000	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr19:53393800-53399800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr19:53393800-53399800	Weak transcription	Osteobl	bone
48	chr19:53393800-53400200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:53394000-53398800	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr19:53394000-53399400	Weak transcription	Spleen	Spleen

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