Variant report

Variant	rs28712197
Chromosome Location	chr3:196107214-196107215
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196106180..196108798-chr3:196131015..196133937,2	K562	blood:
2	chr3:196100863..196102886-chr3:196104953..196107824,2	K562	blood:
3	chr3:196105489..196108118-chr3:196158245..196159887,2	K562	blood:

Variant related genes	Relation type
ENSG00000225822	Chromatin interaction
ENSG00000163960	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12637868	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34801745	0.94[ASN][1000 genomes]
rs35959625	0.93[ASN][1000 genomes]
rs3973	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4459932	0.89[ASN][1000 genomes]
rs4577498	0.82[ASN][1000 genomes]
rs4916427	0.82[EUR][1000 genomes]
rs4916492	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4916493	0.83[ASN][1000 genomes]
rs61345811	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6583305	0.82[ASN][1000 genomes]
rs6774894	0.94[ASN][1000 genomes]
rs7372674	0.86[ASN][1000 genomes]
rs7618690	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9846106	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9867369	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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

No data

Chromatin state (count:122 , 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	chr3:196086400-196116000	Weak transcription	A549	lung
5	chr3:196088400-196116600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:196089400-196116400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:196089600-196113600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:196089600-196115600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr3:196089600-196150000	Weak transcription	Small Intestine	intestine
10	chr3:196089800-196109200	Weak transcription	Fetal Brain Male	brain
11	chr3:196089800-196115800	Weak transcription	HUVEC	blood vessel
12	chr3:196089800-196116200	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:196094000-196116400	Weak transcription	Gastric	stomach
14	chr3:196094000-196126200	Weak transcription	Colonic Mucosa	Colon
15	chr3:196094200-196116400	Weak transcription	Esophagus	oesophagus
16	chr3:196094800-196115400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:196094800-196115800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:196094800-196115800	Weak transcription	Brain Angular Gyrus	brain
19	chr3:196095000-196115400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr3:196095000-196115400	Weak transcription	NH-A	brain
21	chr3:196095600-196144400	Weak transcription	Fetal Heart	heart
22	chr3:196096400-196115400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:196098000-196126800	Weak transcription	Pancreas	Pancrea
24	chr3:196098200-196116000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:196098200-196116000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:196098400-196117000	Weak transcription	Brain Substantia Nigra	brain
27	chr3:196098600-196117000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:196098800-196116000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:196099000-196115400	Weak transcription	HMEC	breast
30	chr3:196099000-196115400	Weak transcription	Osteobl	bone
31	chr3:196099400-196115400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:196099600-196116000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:196102000-196115400	Weak transcription	HSMM	muscle
34	chr3:196102000-196117200	Weak transcription	NHEK	skin
35	chr3:196102400-196108400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:196102400-196108400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:196104000-196107800	Strong transcription	Primary B cells from peripheral blood	blood
38	chr3:196104400-196107800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:196104400-196115400	Weak transcription	NHDF-Ad	bronchial
40	chr3:196104800-196107600	Strong transcription	Stomach Smooth Muscle	stomach
41	chr3:196105200-196108400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:196105200-196108600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr3:196105400-196107800	Strong transcription	HepG2	liver
44	chr3:196105400-196108000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:196105600-196116400	Weak transcription	Spleen	Spleen
46	chr3:196106000-196107400	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr3:196106000-196107800	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:196106000-196108400	Strong transcription	Fetal Lung	lung
49	chr3:196106000-196108400	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr3:196106000-196108600	Strong transcription	Rectal Mucosa Donor 29	rectum

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