Variant report

Variant	rs7616433
Chromosome Location	chr3:196015423-196015424
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:196014121-196015468	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr3:196013746-196016683	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr3:196015392-196016026	K562	blood:	n/a	n/a
4	MAZ	chr3:196013703-196015449	IMR90	lung:	n/a	chr3:196014268-196014278
5	MAX	chr3:196013964-196015474	A549	lung:	n/a	chr3:196014268-196014278
6	REST	chr3:196013834-196015425	H1-neurons	neurons:	n/a	chr3:196014757-196014770 chr3:196014969-196014979
7	POLR2A	chr3:196013879-196015732	MCF-7	breast:	n/a	n/a
8	POLR2A	chr3:196013987-196015736	MCF-7	breast:	n/a	n/a
9	MXI1	chr3:196013686-196016157	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr3:196015383-196015771	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:196013997-196015795	K562	blood:	n/a	n/a
12	MAX	chr3:196013835-196015500	ECC-1	luminal epithelium:	n/a	chr3:196014268-196014278
13	POLR2A	chr3:196015417-196015558	MCF-7	breast:	n/a	n/a
14	MAX	chr3:196013781-196015471	ECC-1	luminal epithelium:	n/a	chr3:196014268-196014278
15	POLR2A	chr3:196014047-196015860	PANC-1	pancreas:	n/a	n/a
16	MXI1	chr3:196013781-196015538	IMR90	lung:	n/a	n/a
17	MAX	chr3:196014006-196015450	MCF-7	breast:	n/a	chr3:196014268-196014278
18	MAX	chr3:196013845-196015447	HepG2	liver:	n/a	chr3:196014268-196014278
19	POLR2A	chr3:196014231-196015648	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr3:196015386-196015783	ECC-1	luminal epithelium:	n/a	n/a
21	SIN3AK20	chr3:196013758-196015541	MCF-7	breast:	n/a	n/a
22	GABPA	chr3:196013816-196015545	MCF-7	breast:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:196012776..196015922-chr3:196063347..196066816,3	MCF-7	breast:
2	chr3:196013519..196016421-chr3:196024534..196027087,2	K562	blood:
3	chr3:196012377..196016502-chr3:196041586..196047553,11	K562	blood:
4	chr3:196013567..196017227-chr3:196043342..196045325,4	MCF-7	breast:
5	chr3:196014537..196016415-chr3:196229117..196231929,2	MCF-7	breast:
6	chr3:196014832..196016725-chr3:196229110..196231842,2	K562	blood:
7	chr3:196013815..196016163-chr6:27090213..27092532,2	MCF-7	breast:
8	chr3:196015046..196017473-chr3:196021246..196023038,2	K562	blood:
9	chr3:196014705..196016276-chr3:196018024..196020194,2	K562	blood:
10	chr3:196014550..196016725-chr3:196229110..196232092,4	K562	blood:
11	chr3:196012352..196016755-chr3:196062622..196069148,9	K562	blood:
12	chr3:196012576..196016636-chr3:196061383..196069148,11	K562	blood:
13	chr3:196014592..196016192-chr3:196157861..196160786,2	MCF-7	breast:
14	chr3:196013508..196016403-chr3:196043043..196046288,6	MCF-7	breast:
15	chr3:196013398..196015851-chr3:196068583..196071493,3	MCF-7	breast:
16	chr3:196014434..196017243-chr3:196157002..196159307,2	K562	blood:

No data

Variant related genes	Relation type
PCYT1A	TF binding region
ENSG00000163960	Chromatin interaction
ENSG00000213123	Chromatin interaction
ENSG00000272741	Chromatin interaction
ENSG00000145107	Chromatin interaction
ENSG00000225822	Chromatin interaction
ENSG00000212146	Chromatin interaction
ENSG00000163961	Chromatin interaction
ENSG00000235897	Chromatin interaction
ENSG00000272468	Chromatin interaction
ENSG00000273331	Chromatin interaction
ENSG00000237418	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11914521	0.86[ASN][1000 genomes]
rs11929532	0.86[ASN][1000 genomes]
rs12637379	0.86[ASN][1000 genomes]
rs1357289	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2293160	0.86[ASN][1000 genomes]
rs4916424	0.86[ASN][1000 genomes]
rs4916425	0.86[ASN][1000 genomes]
rs4916477	0.86[ASN][1000 genomes]
rs4916480	0.91[AFR][1000 genomes]
rs55878253	0.86[ASN][1000 genomes]
rs56240083	0.86[ASN][1000 genomes]
rs56370923	0.86[ASN][1000 genomes]
rs60216585	0.86[ASN][1000 genomes]
rs60336404	0.86[ASN][1000 genomes]
rs67317524	0.86[ASN][1000 genomes]
rs67600689	0.86[ASN][1000 genomes]
rs6762272	0.86[ASN][1000 genomes]
rs6766480	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6778879	0.86[ASN][1000 genomes]
rs6809764	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73212160	0.86[ASN][1000 genomes]
rs7616515	0.86[AFR][1000 genomes]
rs7631913	0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv878179	chr3:195929268-196019680	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
14	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
15	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
16	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
17	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
18	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
19	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7616433	TM4SF19	cis	Muscle Skeletal	GTEx
rs7616433	TM4SF19-AS1	cis	Muscle Skeletal	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196012400-196015600	Active TSS	HSMMtube	muscle
2	chr3:196012600-196015800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr3:196012800-196015600	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr3:196013000-196015600	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr3:196013000-196015600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:196013000-196015600	Active TSS	Small Intestine	intestine
7	chr3:196013200-196015600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:196013200-196015600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:196013200-196015600	Active TSS	Fetal Intestine Small	intestine
10	chr3:196013200-196015600	Active TSS	Left Ventricle	heart
11	chr3:196013200-196015600	Active TSS	Psoas Muscle	Psoas
12	chr3:196013200-196015600	Active TSS	Right Ventricle	heart
13	chr3:196013200-196015800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:196013400-196015600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:196013400-196015600	Active TSS	Muscle Satellite Cultured Cells	--
16	chr3:196013400-196015600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:196013400-196015600	Active TSS	GM12878-XiMat	blood
18	chr3:196013400-196015600	Active TSS	K562	blood
19	chr3:196013400-196015800	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr3:196013400-196015800	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr3:196013400-196015800	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr3:196013400-196015800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:196013400-196015800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:196013400-196015800	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr3:196013400-196015800	Active TSS	A549	lung
26	chr3:196013400-196015800	Active TSS	HSMM	muscle
27	chr3:196013400-196015800	Active TSS	NHEK	skin
28	chr3:196013400-196016000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:196013600-196015600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:196013600-196015600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:196013600-196015600	Active TSS	Brain Angular Gyrus	brain
32	chr3:196013600-196015600	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr3:196013600-196015600	Active TSS	HUVEC	blood vessel
34	chr3:196013600-196015800	Active TSS	H1 Cell Line	embryonic stem cell
35	chr3:196013600-196015800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:196013600-196015800	Active TSS	Fetal Intestine Large	intestine
37	chr3:196013600-196015800	Active TSS	Stomach Smooth Muscle	stomach
38	chr3:196013800-196015600	Active TSS	H9 Cell Line	embryonic stem cell
39	chr3:196013800-196015600	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr3:196013800-196015600	Active TSS	Fetal Stomach	stomach
41	chr3:196013800-196015600	Active TSS	Ovary	ovary
42	chr3:196013800-196015600	Active TSS	Placenta Amnion	Placenta Amnion
43	chr3:196013800-196015800	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr3:196014000-196015600	Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr3:196014000-196015600	Active TSS	Brain Anterior Caudate	brain
46	chr3:196014000-196015600	Active TSS	Thymus	Thymus
47	chr3:196014000-196015600	Active TSS	Monocytes-CD14+_RO01746	blood
48	chr3:196014000-196015800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:196014000-196015800	Active TSS	Duodenum Mucosa	Duodenum
50	chr3:196014000-196015800	Active TSS	Hela-S3	cervix

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