Variant report

Variant	rs17716261
Chromosome Location	chr20:1146048-1146049
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:1145584-1156228	HepG2	liver:	n/a	n/a
2	RCOR1	chr20:1145769-1146070	K562	blood:	n/a	n/a
3	POLR2A	chr20:1146003-1146213	HepG2	liver:	n/a	n/a
4	TAL1	chr20:1145739-1146053	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr20:1146033-1146083	H1-hESC	embryonic stem cell:	embryo
2	chr20:1146033-1146083	HUVEC	blood vessel:	n/a
3	chr20:1146033-1146083	HNPCEpiC	eye:	n/a
4	chr20:1146033-1146083	BE2_C	brain:	n/a
5	chr20:1146033-1146083	LNCaP	prostate:	n/a
6	chr20:1146033-1146083	GM12878	blood:	n/a
7	chr20:1146033-1146083	BJ	skin:	n/a
8	chr20:1146033-1146083	PFSK-1	brain:	n/a
9	chr20:1146033-1146083	Jurkat	blood:	n/a
10	chr20:1146033-1146083	NH-A	brain:	n/a
11	chr20:1146033-1146083	HRPEpiC	eye:	n/a
12	chr20:1146033-1146083	Hela-S3	cervix:	n/a
13	chr20:1146033-1146083	AG04450	lung:	fetal
14	chr20:1146033-1146083	NHDF-neo	bronchial:	n/a
15	chr20:1146033-1146083	HRCEpiC	kidney:	n/a
16	chr20:1146033-1146083	AG10803	skin:	n/a
17	chr20:1146033-1146083	T-47D	breast:	n/a
18	chr20:1146033-1146083	PrEC	prostate:	n/a
19	chr20:1146033-1146083	ovcar-3	ovarian:	n/a
20	chr20:1146033-1146083	AoSMC	blood vessel:	n/a
21	chr20:1146033-1146083	HMEC	breast:	n/a
22	chr20:1146033-1146083	GM19239	blood:	n/a
23	chr20:1146033-1146083	NB4	blood:	n/a
24	chr20:1146033-1146083	HPAEpiC	pulmonary alveolar:	n/a
25	chr20:1146033-1146083	PANC-1	pancreas:	n/a
26	chr20:1146033-1146083	K562	blood:	n/a
27	chr20:1146033-1146083	HRE	kidney:	n/a
28	chr20:1146033-1146083	AG09319	gingival:	n/a
29	chr20:1146033-1146083	CMK	blood:	n/a
30	chr20:1146033-1146083	GM12892	blood:	n/a
31	chr20:1146033-1146083	HEEpiC	esophagus:	n/a
32	chr20:1146033-1146083	HCPEpiC	choroid plexus:	n/a
33	chr20:1146033-1146083	MCF10A-Er-Src	breast:	n/a
34	chr20:1146033-1146083	IMR90	lung:	fetal
35	chr20:1146033-1146083	AG04449	skin:	fetal
36	chr20:1146033-1146083	HCF	heart:	n/a
37	chr20:1146033-1146083	U87	brain:	n/a
38	chr20:1146033-1146083	SK-N-MC	brain:	n/a
39	chr20:1146033-1146083	GM06990	blood:	n/a
40	chr20:1146033-1146083	HL-60	blood:	n/a
41	chr20:1146033-1146083	A549	lung:	n/a
42	chr20:1146033-1146083	MCF-7	breast:	n/a
43	chr20:1146033-1146083	ProgFib	skin:	n/a
44	chr20:1146033-1146083	NHBE	bronchial:	n/a
45	chr20:1146033-1146083	HepG2	liver:	n/a
46	chr20:1146033-1146083	HCT-116	colon:	n/a
47	chr20:1146033-1146083	SKMC	muscle:	n/a
48	chr20:1146033-1146083	NT2-D1	testis:	n/a
49	chr20:1146033-1146083	HCM	heart:	n/a
50	chr20:1146033-1146083	SK-N-SH	brain:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1099167..1103189-chr20:1144544..1147545,4	K562	blood:
2	chr20:1144404..1146146-chr20:1146841..1149612,2	K562	blood:

No data

Variant related genes	Relation type
PSMF1	TF binding region
PSMF1	CpG island
ENSG00000125818	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs17717581	1.00[ASW][hapmap]
rs55813776	1.00[AFR][1000 genomes]
rs55925447	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531450	chr20:809607-1221836	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1058524	chr20:821434-1254865	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv544138	chr20:821434-1254865	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1057939	chr20:824980-1316778	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1065838	chr20:866302-1147601	Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv544139	chr20:866302-1147601	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1059611	chr20:867911-1158694	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv544140	chr20:867911-1158694	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv912585	chr20:992713-1210647	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv1057097	chr20:1030940-1314265	Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1100400-1146600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr20:1112400-1154800	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr20:1113800-1159000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr20:1115200-1153600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr20:1130000-1157800	Strong transcription	Duodenum Mucosa	Duodenum
6	chr20:1132000-1152000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr20:1133800-1153800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr20:1135600-1159800	Weak transcription	Fetal Heart	heart
9	chr20:1136600-1146400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr20:1137200-1148600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr20:1137200-1154400	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr20:1137400-1157800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr20:1137400-1157800	Strong transcription	Thymus	Thymus
14	chr20:1137400-1159200	Strong transcription	Primary T cells from cord blood	blood
15	chr20:1138800-1154600	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr20:1138800-1156800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr20:1138800-1158800	Strong transcription	Fetal Stomach	stomach
18	chr20:1139000-1151200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr20:1139000-1153200	Strong transcription	Dnd41	blood
20	chr20:1139000-1157800	Strong transcription	Liver	Liver
21	chr20:1139000-1157800	Strong transcription	Fetal Muscle Trunk	muscle
22	chr20:1139000-1157800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr20:1139000-1158400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr20:1139200-1152000	Strong transcription	Fetal Thymus	thymus
25	chr20:1139200-1155200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr20:1139600-1157000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr20:1139800-1153800	Strong transcription	A549	lung
28	chr20:1139800-1158200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr20:1140000-1146600	Strong transcription	Lung	lung
30	chr20:1140000-1147400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr20:1140000-1152400	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr20:1140000-1152600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr20:1140000-1152800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr20:1140000-1157800	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr20:1140200-1150800	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr20:1140200-1151200	Strong transcription	HMEC	breast
37	chr20:1140200-1152400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr20:1140200-1152400	Strong transcription	Osteobl	bone
39	chr20:1140200-1153800	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr20:1140200-1154000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr20:1140200-1154800	Strong transcription	Fetal Intestine Large	intestine
42	chr20:1140200-1156400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr20:1140200-1156800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr20:1140200-1156800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr20:1140200-1157600	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr20:1140200-1157800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr20:1140200-1157800	Strong transcription	Fetal Muscle Leg	muscle
48	chr20:1140200-1158400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr20:1140200-1159000	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr20:1140400-1146400	Strong transcription	NH-A	brain

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