Variant report

Variant	rs4723892
Chromosome Location	chr7:39746466-39746467
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:39745397..39755065-chr7:39757582..39762895,14	K562	blood:
2	chr7:39663965..39666888-chr7:39745709..39748529,2	K562	blood:
3	chr7:39661494..39663299-chr7:39746333..39747974,2	MCF-7	breast:
4	chr7:39744986..39746903-chr7:39768922..39771853,2	K562	blood:

Variant related genes	Relation type
ENSG00000006451	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11767632	0.95[CEU][hapmap]
rs11769865	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs11982634	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs2107710	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs2158548	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2158549	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189837	0.93[EUR][1000 genomes]
rs2329464	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2876862	0.90[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3823742	0.93[EUR][1000 genomes]
rs4723887	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4723891	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6462937	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs6952363	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6952866	0.89[EUR][1000 genomes]
rs6956681	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6961667	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6969070	0.89[EUR][1000 genomes]
rs6969523	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs7785049	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7806651	0.84[EUR][1000 genomes]
rs917077	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv427777	chr7:39726513-39936904	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4723892	LINC00265	cis	Thyroid	GTEx
rs4723892	LINC00265	cis	lung	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39715200-39749400	Weak transcription	Aorta	Aorta
2	chr7:39727400-39747800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr7:39730600-39749200	Weak transcription	Ovary	ovary
4	chr7:39732000-39748000	Strong transcription	HUVEC	blood vessel
5	chr7:39732000-39749200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:39736600-39749400	Weak transcription	Fetal Heart	heart
7	chr7:39737400-39749800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr7:39737600-39748800	Weak transcription	Colon Smooth Muscle	Colon
9	chr7:39737800-39749400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr7:39737800-39749400	Weak transcription	Psoas Muscle	Psoas
11	chr7:39738000-39748600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:39738000-39749200	Weak transcription	Fetal Brain Female	brain
13	chr7:39738000-39749400	Weak transcription	Placenta	Placenta
14	chr7:39738400-39748400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr7:39738600-39748800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr7:39738600-39748800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr7:39738600-39749200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr7:39739600-39749600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr7:39740200-39747200	Weak transcription	Gastric	stomach
20	chr7:39740200-39748000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr7:39740200-39749200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr7:39740200-39749400	Weak transcription	Pancreas	Pancrea
23	chr7:39740200-39749400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr7:39740200-39749600	Weak transcription	Lung	lung
25	chr7:39740200-39752000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr7:39740400-39747400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr7:39740400-39749000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr7:39740400-39749600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr7:39740600-39748200	Weak transcription	Brain Anterior Caudate	brain
30	chr7:39740600-39749400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr7:39740600-39749400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr7:39740800-39747800	Weak transcription	Right Ventricle	heart
33	chr7:39740800-39748600	Weak transcription	Fetal Thymus	thymus
34	chr7:39740800-39749000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr7:39740800-39749200	Weak transcription	Brain Germinal Matrix	brain
36	chr7:39740800-39749200	Weak transcription	GM12878-XiMat	blood
37	chr7:39740800-39749200	Weak transcription	NHLF	lung
38	chr7:39740800-39749400	Weak transcription	Thymus	Thymus
39	chr7:39741000-39748600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr7:39741000-39749200	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr7:39741200-39748200	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr7:39741200-39748600	Weak transcription	Fetal Lung	lung
43	chr7:39741200-39748800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr7:39741200-39749400	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr7:39741200-39749600	Weak transcription	Dnd41	blood
46	chr7:39741200-39753000	Weak transcription	Spleen	Spleen
47	chr7:39741400-39748800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr7:39741400-39749200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr7:39741600-39746800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr7:39741600-39747400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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