Variant report

Variant	rs6583305
Chromosome Location	chr3:196118621-196118622
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	chr3:196116600..196119227-chr3:196123432..196124939,2	K562	blood:

Variant related genes	Relation type
ENSG00000241868	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12637868	0.83[ASN][1000 genomes]
rs28712197	0.82[ASN][1000 genomes]
rs34801745	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35959625	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4459932	1.00[CEU][hapmap];0.87[CHB][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4577498	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4916427	0.88[CHB][hapmap]
rs4916492	0.81[ASN][1000 genomes]
rs4916493	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61345811	0.82[ASN][1000 genomes]
rs6764533	1.00[CEU][hapmap];0.94[CHB][hapmap]
rs6772164	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs6774894	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7372674	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7618690	0.81[ASN][1000 genomes]
rs7639524	0.82[JPT][hapmap]
rs9841810	0.82[JPT][hapmap]
rs9846106	0.86[ASN][1000 genomes]
rs9847223	0.82[JPT][hapmap]
rs9860931	0.82[JPT][hapmap]
rs9867369	0.94[AMR][1000 genomes];0.98[EUR][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	nsv965351	chr3:196116295-196122043	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6583305	TM4SF19	cis	Muscle Skeletal	GTEx
rs6583305	TM4SF19-AS1	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 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	chr3:196113200-196120000	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr3:196113200-196136400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:196113400-196119600	Weak transcription	Fetal Brain Male	brain
12	chr3:196115000-196118800	Strong transcription	Fetal Muscle Leg	muscle
13	chr3:196115000-196121000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:196115200-196118800	Strong transcription	Primary hematopoietic stem cells	blood
15	chr3:196115200-196119800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:196115200-196120200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:196115400-196118800	Strong transcription	Fetal Lung	lung
18	chr3:196115400-196118800	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr3:196115400-196118800	Strong transcription	HSMM	muscle
20	chr3:196115400-196118800	Strong transcription	K562	blood
21	chr3:196115400-196119200	Strong transcription	Fetal Intestine Large	intestine
22	chr3:196115400-196119400	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:196115400-196119400	Strong transcription	Thymus	Thymus
24	chr3:196115400-196119800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:196115400-196120000	Strong transcription	Primary B cells from cord blood	blood
26	chr3:196115400-196120000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:196115400-196120000	Strong transcription	Fetal Muscle Trunk	muscle
28	chr3:196115400-196120200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr3:196115400-196120600	Strong transcription	Primary B cells from peripheral blood	blood
30	chr3:196115400-196120600	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr3:196115400-196120600	Strong transcription	Adipose Nuclei	Adipose
32	chr3:196115400-196120800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:196115400-196120800	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr3:196115400-196120800	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr3:196115400-196120800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr3:196115400-196121000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:196115400-196121000	Strong transcription	Fetal Thymus	thymus
38	chr3:196115400-196121600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:196115400-196126400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:196115400-196127800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:196115400-196127800	Strong transcription	Placenta	Placenta
42	chr3:196115400-196127800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr3:196115400-196129800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr3:196115600-196119000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
45	chr3:196115600-196119400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:196115600-196120000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:196115600-196120400	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:196115600-196121600	Strong transcription	Dnd41	blood
49	chr3:196115600-196134600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:196115800-196118800	Strong transcription	Duodenum Mucosa	Duodenum

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