Variant report

Variant	rs6774894
Chromosome Location	chr3:196116393-196116394
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	chr3:196115479..196118192-chr3:196129291..196130932,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12637868	0.96[ASN][1000 genomes]
rs28712197	0.94[ASN][1000 genomes]
rs34801745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35959625	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3973	0.99[ASN][1000 genomes]
rs4459932	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4577498	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4916492	0.93[ASN][1000 genomes]
rs4916493	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61345811	0.94[ASN][1000 genomes]
rs6583305	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7372674	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7618690	0.93[ASN][1000 genomes]
rs9846106	0.99[ASN][1000 genomes]
rs9867369	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[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	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
rs6774894	TM4SF19-AS1	cis	Muscle Skeletal	GTEx
rs6774894	TM4SF19	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	chr3:196088400-196116600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:196089400-196116400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:196089600-196150000	Weak transcription	Small Intestine	intestine
7	chr3:196094000-196116400	Weak transcription	Gastric	stomach
8	chr3:196094000-196126200	Weak transcription	Colonic Mucosa	Colon
9	chr3:196094200-196116400	Weak transcription	Esophagus	oesophagus
10	chr3:196095600-196144400	Weak transcription	Fetal Heart	heart
11	chr3:196098000-196126800	Weak transcription	Pancreas	Pancrea
12	chr3:196098400-196117000	Weak transcription	Brain Substantia Nigra	brain
13	chr3:196098600-196117000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:196102000-196117200	Weak transcription	NHEK	skin
15	chr3:196105600-196116400	Weak transcription	Spleen	Spleen
16	chr3:196106600-196116400	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:196107400-196116400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:196107600-196116400	Weak transcription	Left Ventricle	heart
19	chr3:196107600-196116400	Weak transcription	Right Ventricle	heart
20	chr3:196107800-196116400	Weak transcription	Aorta	Aorta
21	chr3:196107800-196116400	Weak transcription	Lung	lung
22	chr3:196108400-196116400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:196108400-196116400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:196111200-196117600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:196113000-196124600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:196113200-196116400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:196113200-196116400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:196113200-196120000	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr3:196113200-196136400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:196113400-196119600	Weak transcription	Fetal Brain Male	brain
31	chr3:196113800-196116400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr3:196114600-196117200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
33	chr3:196114800-196118000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:196115000-196116600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
35	chr3:196115000-196118800	Strong transcription	Fetal Muscle Leg	muscle
36	chr3:196115000-196121000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr3:196115200-196117800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:196115200-196118800	Strong transcription	Primary hematopoietic stem cells	blood
39	chr3:196115200-196119800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:196115200-196120200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:196115400-196116400	Enhancers	Muscle Satellite Cultured Cells	--
42	chr3:196115400-196116600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:196115400-196116800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
44	chr3:196115400-196117200	Strong transcription	HMEC	breast
45	chr3:196115400-196117400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:196115400-196118000	ZNF genes & repeats	GM12878-XiMat	blood
47	chr3:196115400-196118600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:196115400-196118600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr3:196115400-196118800	Strong transcription	Fetal Lung	lung
50	chr3:196115400-196118800	Strong transcription	Rectal Mucosa Donor 29	rectum

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