Variant report

Variant	rs4916425
Chromosome Location	chr3:196024719-196024720
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:196013519..196016421-chr3:196024534..196027087,2	K562	blood:
2	chr3:196022549..196024808-chr3:196044443..196046676,2	K562	blood:

Variant related genes	Relation type
ENSG00000213123	Chromatin interaction
ENSG00000235897	Chromatin interaction
ENSG00000161217	Chromatin interaction
ENSG00000272741	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11914521	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11929532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629949	0.80[ASN][1000 genomes]
rs12633502	0.83[ASN][1000 genomes]
rs12637288	0.89[CHD][hapmap];0.85[JPT][hapmap]
rs12637379	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1357289	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs1948690	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2047550	0.88[CHB][hapmap];0.96[CHD][hapmap]
rs2047551	0.89[CHD][hapmap];0.85[JPT][hapmap]
rs2088666	0.89[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2270769	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2293160	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772109	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs4396926	0.81[ASN][1000 genomes]
rs4916421	0.89[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4916424	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916456	0.81[ASN][1000 genomes]
rs4916476	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4916477	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916479	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4916485	0.88[CHB][hapmap];0.96[CHD][hapmap];0.83[ASN][1000 genomes]
rs55878253	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55903345	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55996879	0.85[ASN][1000 genomes]
rs56240083	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56370923	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58297632	0.81[ASN][1000 genomes]
rs59352354	0.81[ASN][1000 genomes]
rs60216585	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60336404	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66487782	0.81[ASN][1000 genomes]
rs66780758	0.81[ASN][1000 genomes]
rs66805306	0.81[ASN][1000 genomes]
rs66927787	0.81[ASN][1000 genomes]
rs66942309	0.83[ASN][1000 genomes]
rs67204670	0.83[ASN][1000 genomes]
rs67317524	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67349960	0.81[ASN][1000 genomes]
rs67600689	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6766480	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6768240	0.81[ASN][1000 genomes]
rs67784045	0.81[ASN][1000 genomes]
rs6778879	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67947474	0.81[ASN][1000 genomes]
rs68056570	0.81[ASN][1000 genomes]
rs6809764	0.97[ASN][1000 genomes]
rs72611188	0.80[ASN][1000 genomes]
rs73212155	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73212160	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73212178	0.83[ASN][1000 genomes]
rs7616433	0.86[ASN][1000 genomes]
rs7631913	0.85[JPT][hapmap]
rs7636149	0.89[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs7640304	0.81[ASN][1000 genomes]
rs9714038	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv461131	chr3:195858887-196072442	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
7	nsv593071	chr3:195858887-196072442	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
8	nsv1009178	chr3:195864466-196081670	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
9	nsv536892	chr3:195864466-196081670	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
10	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
11	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
12	nsv1014563	chr3:195934010-196085951	Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
13	nsv878180	chr3:195946535-196066569	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS 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	33 gene(s)	inside rSNPs	diseases
14	nsv878181	chr3:195946535-196072442	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
15	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
16	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
17	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4916425	TM4SF19	cis	Muscle Skeletal	GTEx
rs4916425	TCTEX1D2	cis	Adipose Subcutaneous	GTEx
rs4916425	TCTEX1D2	cis	Artery Tibial	GTEx
rs4916425	TCTEX1D2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196015200-196038800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:196015200-196044400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:196015400-196028800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:196015400-196030200	Weak transcription	NHDF-Ad	bronchial
5	chr3:196015400-196033000	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:196015400-196043800	Weak transcription	Brain Substantia Nigra	brain
7	chr3:196015400-196043800	Weak transcription	Fetal Kidney	kidney
8	chr3:196015400-196043800	Weak transcription	Fetal Lung	lung
9	chr3:196015400-196044400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:196015400-196044400	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:196015400-196044400	Weak transcription	Lung	lung
12	chr3:196015600-196026200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:196015600-196026200	Weak transcription	Thymus	Thymus
14	chr3:196015600-196026400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:196015600-196026800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:196015600-196026800	Weak transcription	Ovary	ovary
17	chr3:196015600-196027800	Weak transcription	Brain Anterior Caudate	brain
18	chr3:196015600-196028200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:196015600-196028800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:196015600-196034200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:196015600-196034400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:196015600-196034800	Weak transcription	HSMMtube	muscle
23	chr3:196015600-196036200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:196015600-196041400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:196015600-196043600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:196015600-196043600	Weak transcription	Fetal Brain Male	brain
27	chr3:196015600-196043800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:196015600-196043800	Weak transcription	Brain Angular Gyrus	brain
29	chr3:196015600-196044200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:196015600-196044200	Weak transcription	Adipose Nuclei	Adipose
31	chr3:196015600-196044400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:196015800-196024800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:196015800-196025600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:196015800-196026200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:196015800-196026800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:196015800-196026800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:196015800-196026800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:196015800-196026800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr3:196015800-196028000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:196015800-196028800	Weak transcription	Osteobl	bone
41	chr3:196015800-196029000	Weak transcription	NHEK	skin
42	chr3:196015800-196038800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr3:196015800-196042800	Weak transcription	HMEC	breast
44	chr3:196015800-196043000	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:196015800-196043400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:196015800-196043600	Weak transcription	A549	lung
47	chr3:196015800-196043800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:196015800-196043800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:196015800-196043800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr3:196015800-196043800	Weak transcription	HSMM	muscle

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