Variant report

Variant	rs6764533
Chromosome Location	chr3:196088464-196088465
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196068603..196070479-chr3:196087744..196090731,2	K562	blood:
2	chr3:196081918..196083846-chr3:196086932..196089024,2	MCF-7	breast:
3	chr3:196087051..196089707-chr3:196092775..196094458,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs3973	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4459932	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4630973	0.88[JPT][hapmap]
rs4916427	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6583305	1.00[CEU][hapmap];0.94[CHB][hapmap]
rs6772164	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6774540	0.88[JPT][hapmap]
rs7373049	0.88[JPT][hapmap]
rs7373103	0.88[JPT][hapmap]
rs9848247	0.86[JPT][hapmap]
rs9877304	0.84[GIH][hapmap]

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	esv3401011	chr3:196086397-196090496	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6764533	TM4SF19-AS1	cis	Muscle Skeletal	GTEx
rs6764533	TM4SF19	cis	Muscle Skeletal	GTEx
rs6764533	TCTEX1D2	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196054600-196091000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:196070600-196106400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:196071800-196100800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:196072400-196099600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:196073600-196135800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:196074200-196099000	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr3:196074800-196099000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:196077000-196100400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:196077600-196089800	Strong transcription	Osteobl	bone
10	chr3:196077800-196093200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:196077800-196095200	Strong transcription	Fetal Muscle Trunk	muscle
12	chr3:196078600-196089800	Strong transcription	Primary T cells from cord blood	blood
13	chr3:196078800-196090000	Strong transcription	Brain Inferior Temporal Lobe	brain
14	chr3:196078800-196095000	Strong transcription	Fetal Muscle Leg	muscle
15	chr3:196079200-196089600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:196079600-196090800	Strong transcription	Fetal Intestine Large	intestine
17	chr3:196079800-196089800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:196079800-196089800	Strong transcription	Adipose Nuclei	Adipose
19	chr3:196079800-196089800	Strong transcription	Liver	Liver
20	chr3:196079800-196091400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:196079800-196096800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:196079800-196099000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:196080000-196089800	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:196080000-196090400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:196080000-196090600	Strong transcription	Placenta	Placenta
26	chr3:196080000-196090600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr3:196080000-196091400	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr3:196080000-196093400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:196080200-196089800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:196080200-196090600	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr3:196080400-196090600	Strong transcription	Fetal Thymus	thymus
32	chr3:196080600-196089800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:196080600-196090000	Strong transcription	Duodenum Mucosa	Duodenum
34	chr3:196080600-196090800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr3:196080600-196095000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:196080600-196100800	Strong transcription	Dnd41	blood
37	chr3:196080800-196089400	Strong transcription	Fetal Brain Female	brain
38	chr3:196080800-196089600	Strong transcription	Brain Hippocampus Middle	brain
39	chr3:196080800-196089600	Strong transcription	HSMMtube	muscle
40	chr3:196080800-196089800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:196080800-196089800	Strong transcription	Primary B cells from cord blood	blood
42	chr3:196080800-196090400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:196080800-196090800	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr3:196080800-196090800	Strong transcription	Ovary	ovary
45	chr3:196080800-196092600	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr3:196081000-196089400	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr3:196081000-196089600	Strong transcription	Brain Substantia Nigra	brain
48	chr3:196081000-196090800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:196081000-196090800	Strong transcription	Primary B cells from peripheral blood	blood
50	chr3:196081000-196091600	Strong transcription	GM12878-XiMat	blood

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