Variant report

Variant	rs4714123
Chromosome Location	chr6:38013738-38013739
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38004599..38007314-chr6:38011024..38013903,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10755700	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13198420	0.86[CHB][hapmap]
rs13437477	0.90[YRI][hapmap]
rs1885325	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1923279	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1979759	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs2180514	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2201646	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs259672	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs259675	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap]
rs259676	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs259678	0.81[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs259683	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs259687	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs259693	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4506034	0.84[ASN][1000 genomes]
rs4711522	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4714118	0.81[EUR][1000 genomes]
rs4714125	0.97[ASN][1000 genomes]
rs6458040	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6458042	0.84[ASN][1000 genomes]
rs67479083	0.80[EUR][1000 genomes]
rs6901928	0.92[YRI][hapmap]
rs6915506	0.81[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs6916091	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6917668	0.94[CEU][hapmap]
rs6920185	0.82[EUR][1000 genomes]
rs6924634	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929371	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6930859	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6934617	0.94[CEU][hapmap]
rs6936504	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6938580	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7751390	0.88[ASN][1000 genomes]
rs7752686	0.92[YRI][hapmap]
rs7765798	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap]
rs881681	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs9349053	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9357261	1.00[YRI][hapmap]
rs9369029	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs9369033	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9380716	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9394469	0.82[EUR][1000 genomes]
rs9462372	0.92[YRI][hapmap]
rs9462374	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9462380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9470723	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs9470724	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs9470759	0.85[YRI][hapmap]
rs9470762	0.90[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9470767	0.88[ASN][1000 genomes]
rs9470800	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9647620	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]

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	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv2763549	chr6:37985025-38014006	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv2754649	chr6:37985025-38147910	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv970298	chr6:38003938-38014330	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4714123	LRFN2	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37985000-38030200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:37995800-38020600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr6:37996000-38015400	Weak transcription	HSMMtube	muscle
4	chr6:37998600-38029200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:37999800-38017600	Weak transcription	Right Atrium	heart
6	chr6:37999800-38018600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:38001000-38028600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:38002400-38029400	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr6:38002800-38017800	Weak transcription	HSMM	muscle
10	chr6:38002800-38024400	Weak transcription	Fetal Stomach	stomach
11	chr6:38003000-38024800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr6:38003000-38025000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr6:38003200-38024400	Weak transcription	Primary T cells from cord blood	blood
14	chr6:38003600-38025400	Weak transcription	NHDF-Ad	bronchial
15	chr6:38003800-38017800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:38004000-38018000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:38004000-38018200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:38004200-38024600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:38004200-38029200	Weak transcription	Primary B cells from cord blood	blood
20	chr6:38006800-38024200	Weak transcription	Thymus	Thymus
21	chr6:38007400-38025400	Weak transcription	NH-A	brain
22	chr6:38007600-38018000	Weak transcription	Osteobl	bone
23	chr6:38008400-38028400	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr6:38009000-38019400	Weak transcription	A549	lung
25	chr6:38009200-38018800	Weak transcription	Right Ventricle	heart
26	chr6:38010400-38013800	Enhancers	HepG2	liver
27	chr6:38010600-38029000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr6:38011600-38013800	Weak transcription	Left Ventricle	heart
29	chr6:38011600-38024200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr6:38011800-38024200	Weak transcription	Psoas Muscle	Psoas
31	chr6:38011800-38029400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:38012000-38022400	Weak transcription	Colon Smooth Muscle	Colon
33	chr6:38012400-38029400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr6:38012600-38016800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr6:38013600-38014000	Enhancers	Liver	Liver

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