Variant report

Variant	rs316402
Chromosome Location	chr5:43073433-43073434
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:43072960..43074687-chr5:43105547..43106356,10	MCF-7	breast:
2	chr5:43042017..43044815-chr5:43072102..43074206,2	K562	blood:
3	chr5:43073404..43075652-chr5:43524042..43526111,2	K562	blood:
4	chr5:43034726..43053192-chr5:43061725..43074206,66	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC114947.1.1-2	chr5:43071269-43076732	XLOC_004366

Variant related genes	Relation type
ENSG00000215068	Chromatin interaction
ENSG00000177721	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10522	0.82[ASN][1000 genomes]
rs13169690	0.81[ASN][1000 genomes]
rs1574407	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs160709	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs178415	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs222060	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2329994	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2603295	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2603636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs316395	0.83[ASN][1000 genomes]
rs316396	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs316400	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs316403	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs316404	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316406	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs316408	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316413	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs316419	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs316422	0.83[ASN][1000 genomes]
rs4092293	0.82[ASN][1000 genomes]
rs4092294	0.82[ASN][1000 genomes]
rs515970	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs543569	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs565761	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs613825	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs643307	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6875214	0.80[ASN][1000 genomes]
rs768441	0.82[ASN][1000 genomes]
rs9292862	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
7	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
8	nsv870299	chr5:43053679-43107880	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs316402	ZNF131	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43068000-43077600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:43068200-43074200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:43068600-43082600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr5:43069000-43081400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:43069200-43074200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr5:43069400-43075800	Strong transcription	Fetal Stomach	stomach
7	chr5:43069400-43082800	Weak transcription	Colonic Mucosa	Colon
8	chr5:43069400-43087400	Weak transcription	Stomach Mucosa	stomach
9	chr5:43069600-43075200	Weak transcription	Fetal Heart	heart
10	chr5:43069600-43077000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:43069600-43080400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr5:43069600-43080400	Strong transcription	Fetal Muscle Leg	muscle
13	chr5:43069800-43076000	Weak transcription	GM12878-XiMat	blood
14	chr5:43070000-43105400	Weak transcription	HSMMtube	muscle
15	chr5:43070200-43073600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:43070200-43077600	Strong transcription	Fetal Intestine Small	intestine
17	chr5:43070400-43075000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr5:43070400-43075200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr5:43070400-43075600	Genic enhancers	Dnd41	blood
20	chr5:43071000-43073600	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr5:43071000-43075600	Strong transcription	Stomach Smooth Muscle	stomach
22	chr5:43071400-43075400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:43071400-43084400	Weak transcription	Fetal Kidney	kidney
24	chr5:43071600-43073600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr5:43071600-43075000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr5:43071600-43079000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:43071600-43079000	Weak transcription	NH-A	brain
28	chr5:43071600-43080800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr5:43071600-43083800	Weak transcription	HepG2	liver
30	chr5:43071600-43084200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr5:43071800-43073600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr5:43071800-43073800	Weak transcription	Fetal Lung	lung
33	chr5:43071800-43073800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr5:43071800-43073800	Weak transcription	K562	blood
35	chr5:43071800-43074200	Weak transcription	Right Ventricle	heart
36	chr5:43071800-43074600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr5:43071800-43074600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr5:43071800-43075000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr5:43071800-43075000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr5:43071800-43075000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr5:43071800-43075000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr5:43071800-43075000	Weak transcription	Brain Angular Gyrus	brain
43	chr5:43071800-43075000	Weak transcription	Brain Anterior Caudate	brain
44	chr5:43071800-43075000	Weak transcription	Lung	lung
45	chr5:43071800-43075000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr5:43071800-43075000	Weak transcription	HUVEC	blood vessel
47	chr5:43071800-43075000	Weak transcription	NHEK	skin
48	chr5:43071800-43075000	Weak transcription	NHLF	lung
49	chr5:43071800-43075200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr5:43071800-43075200	Weak transcription	Brain Hippocampus Middle	brain

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