Variant report

Variant	rs4459932
Chromosome Location	chr3:196141661-196141662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196141592..196145403-chr3:196157124..196159775,4	MCF-7	breast:
2	chr3:196136760..196139527-chr3:196139977..196142790,2	K562	blood:
3	chr3:196044447..196045990-chr3:196139208..196141957,2	MCF-7	breast:
4	chr3:196141252..196144269-chr3:196156132..196159326,3	K562	blood:
5	chr3:196136134..196138094-chr3:196139731..196142693,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235897	Chromatin interaction
ENSG00000213123	Chromatin interaction
ENSG00000163960	Chromatin interaction
ENSG00000225822	Chromatin interaction
ENSG00000272741	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12637868	0.90[ASN][1000 genomes]
rs28712197	0.89[ASN][1000 genomes]
rs34801745	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35959625	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3973	0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4577498	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4630973	0.88[JPT][hapmap]
rs4916427	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs4916492	0.88[ASN][1000 genomes]
rs4916493	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61345811	1.00[ASN][1000 genomes]
rs6583305	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]
rs6764533	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]
rs6772164	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6774540	0.88[JPT][hapmap]
rs6774894	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7372674	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7373049	0.88[JPT][hapmap]
rs7373103	0.88[JPT][hapmap]
rs7618690	0.99[ASN][1000 genomes]
rs9846106	0.96[ASN][1000 genomes]
rs9848247	0.86[JPT][hapmap]
rs9867369	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4459932	TM4SF19	cis	Muscle Skeletal	GTEx
rs4459932	TM4SF19-AS1	cis	Muscle Skeletal	GTEx
rs4459932	TCTEX1D2	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196083600-196143800	Weak transcription	Psoas Muscle	Psoas
2	chr3:196089600-196150000	Weak transcription	Small Intestine	intestine
3	chr3:196095600-196144400	Weak transcription	Fetal Heart	heart
4	chr3:196118600-196157400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:196124600-196147400	Weak transcription	Right Atrium	heart
6	chr3:196125200-196157400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:196127000-196153800	Weak transcription	NHEK	skin
8	chr3:196127400-196152600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr3:196127600-196142800	Weak transcription	Spleen	Spleen
10	chr3:196127600-196145000	Weak transcription	Right Ventricle	heart
11	chr3:196127600-196147600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:196127600-196157400	Weak transcription	HUVEC	blood vessel
13	chr3:196128000-196149800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:196129800-196144800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:196132200-196145800	Weak transcription	Lung	lung
16	chr3:196132200-196153800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr3:196132400-196150000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:196132600-196150000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:196132600-196157400	Weak transcription	Liver	Liver
20	chr3:196134000-196143000	Weak transcription	Ovary	ovary
21	chr3:196134000-196144200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:196134000-196144400	Weak transcription	Fetal Stomach	stomach
23	chr3:196134000-196147800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:196134000-196149800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr3:196134000-196150000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:196134000-196152600	Weak transcription	Fetal Intestine Large	intestine
27	chr3:196134000-196153800	Weak transcription	Primary B cells from cord blood	blood
28	chr3:196134000-196154400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:196134200-196145400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:196134200-196146400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:196134200-196146400	Weak transcription	Brain Anterior Caudate	brain
32	chr3:196134200-196146400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:196134200-196147600	Weak transcription	K562	blood
34	chr3:196134200-196149200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr3:196134200-196149600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr3:196134200-196149600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:196134200-196150000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:196134200-196153800	Weak transcription	Hela-S3	cervix
39	chr3:196134200-196154600	Weak transcription	Dnd41	blood
40	chr3:196134200-196157400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:196134400-196149400	Weak transcription	HSMM	muscle
42	chr3:196134400-196150400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:196134600-196145200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr3:196134600-196157800	Weak transcription	A549	lung
45	chr3:196136000-196149800	Weak transcription	Fetal Lung	lung
46	chr3:196136200-196145200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:196136200-196149600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:196136600-196145400	Weak transcription	Fetal Brain Male	brain
49	chr3:196136600-196150000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:196136600-196156800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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