Variant report

Variant	rs9839978
Chromosome Location	chr3:196122801-196122802
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr3:196122491-196122826	IMR90	lung:	n/a	n/a
2	CEBPB	chr3:196122476-196122834	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr3:196122576-196122820	HepG2	liver:	n/a	n/a
4	CEBPB	chr3:196122622-196122817	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:196122393..196124913-chr3:196156464..196158992,2	K562	blood:

Variant related genes	Relation type
RNU6-1279P	TF binding region
RN7SL738P	TF binding region
ENSG00000225822	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10881567	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11185537	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12488531	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12638961	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13073879	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13089205	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28549737	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28594421	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35561509	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4133244	0.83[AMR][1000 genomes]
rs4290832	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4579046	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6583303	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73213970	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7373049	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7373103	0.84[EUR][1000 genomes]
rs7373385	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7374841	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7624107	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9821735	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9841810	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9847223	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9874783	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
4	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
5	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats 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	64 gene(s)	inside rSNPs	diseases
7	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
8	nsv1003764	chr3:196028141-196190687	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv536895	chr3:196028141-196190687	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
10	esv1844755	chr3:196057616-196190350	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv469831	chr3:196071603-196235225	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	nsv482542	chr3:196071603-196235225	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS 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	28 gene(s)	inside rSNPs	diseases
13	nsv878183	chr3:196072442-196181228	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
14	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
15	esv32642	chr3:196118819-196153861	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196073600-196135800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:196083600-196143800	Weak transcription	Psoas Muscle	Psoas
3	chr3:196084600-196131600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:196089600-196150000	Weak transcription	Small Intestine	intestine
5	chr3:196094000-196126200	Weak transcription	Colonic Mucosa	Colon
6	chr3:196095600-196144400	Weak transcription	Fetal Heart	heart
7	chr3:196098000-196126800	Weak transcription	Pancreas	Pancrea
8	chr3:196113000-196124600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:196113200-196136400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:196115400-196126400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:196115400-196127800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:196115400-196127800	Strong transcription	Placenta	Placenta
13	chr3:196115400-196127800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr3:196115400-196129800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr3:196115600-196134600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:196115800-196125400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:196116000-196126200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:196116200-196126800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:196116200-196129200	Strong transcription	Fetal Stomach	stomach
20	chr3:196116200-196134000	Strong transcription	Fetal Intestine Small	intestine
21	chr3:196116600-196126400	Weak transcription	A549	lung
22	chr3:196116600-196131800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:196116600-196133600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:196117200-196126200	Weak transcription	HMEC	breast
25	chr3:196117200-196126600	Weak transcription	Gastric	stomach
26	chr3:196117200-196126800	Weak transcription	Right Ventricle	heart
27	chr3:196117800-196123800	Weak transcription	HepG2	liver
28	chr3:196117800-196127800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:196117800-196131600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:196118000-196133600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:196118000-196134800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:196118200-196126200	Weak transcription	NHEK	skin
33	chr3:196118600-196123800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:196118600-196124000	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:196118600-196124000	Weak transcription	Fetal Brain Female	brain
36	chr3:196118600-196124400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:196118600-196124800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr3:196118600-196124800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr3:196118600-196125000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr3:196118600-196126200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr3:196118600-196157400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr3:196118800-196123800	Weak transcription	HSMMtube	muscle
43	chr3:196118800-196124000	Weak transcription	Colon Smooth Muscle	Colon
44	chr3:196118800-196124000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr3:196118800-196124000	Weak transcription	Fetal Muscle Leg	muscle
46	chr3:196118800-196124200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr3:196118800-196124200	Weak transcription	Fetal Lung	lung
48	chr3:196118800-196124200	Weak transcription	Osteobl	bone
49	chr3:196118800-196124400	Weak transcription	Esophagus	oesophagus
50	chr3:196118800-196124600	Weak transcription	Fetal Kidney	kidney

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