Variant report

Variant	rs4723885
Chromosome Location	chr7:39649456-39649457
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C7orf11-6	chr7:39649209-39649494	ENSG00000231951.1
2	lnc-YAE1D1-1	chr7:39649086-39651687	NONHSAT120210
3	lnc-YAE1D1-1	chr7:39649316-39649879	NONHSAT120212

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10245247	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10258946	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10266149	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10486798	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486800	0.81[EUR][1000 genomes]
rs12111908	0.98[ASN][1000 genomes]
rs17171603	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs17713754	0.82[ASN][1000 genomes]
rs17713951	0.86[ASN][1000 genomes]
rs17714049	0.98[ASN][1000 genomes]
rs17770594	0.82[ASN][1000 genomes]
rs17770612	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs17770625	0.82[ASN][1000 genomes]
rs1989533	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329455	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2329460	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2329461	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329462	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4469364	0.81[AFR][1000 genomes]
rs4720329	0.84[AFR][1000 genomes]
rs4723881	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4723882	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723883	1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58299139	0.82[ASN][1000 genomes]
rs59071947	0.82[ASN][1000 genomes]
rs61493712	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6958662	0.84[AFR][1000 genomes]
rs6968742	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73375695	0.82[ASN][1000 genomes]
rs7777173	0.83[EUR][1000 genomes]
rs7785964	0.82[ASN][1000 genomes]
rs7796063	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7809088	0.84[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887970	chr7:39587912-39688152	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39644800-39649800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:39645200-39661600	Weak transcription	A549	lung
3	chr7:39646400-39650000	Enhancers	Stomach Mucosa	stomach
4	chr7:39647000-39649800	Enhancers	Hela-S3	cervix
5	chr7:39647600-39650000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:39647600-39650200	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr7:39647800-39649800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr7:39648000-39649800	Enhancers	Small Intestine	intestine
9	chr7:39648000-39649800	Enhancers	HSMM	muscle
10	chr7:39648000-39650000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr7:39648400-39651800	Flanking Active TSS	HUVEC	blood vessel
12	chr7:39648600-39649600	Flanking Active TSS	HMEC	breast
13	chr7:39648600-39649800	Enhancers	Spleen	Spleen
14	chr7:39648600-39649800	Flanking Active TSS	NH-A	brain
15	chr7:39648600-39650000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
16	chr7:39648800-39656000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:39649000-39649600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
18	chr7:39649000-39649600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr7:39649000-39649600	Active TSS	H9 Cell Line	embryonic stem cell
20	chr7:39649000-39649600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
21	chr7:39649000-39649600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
22	chr7:39649000-39649600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
23	chr7:39649000-39649600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
24	chr7:39649000-39649600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr7:39649000-39649600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr7:39649000-39649600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
27	chr7:39649000-39649600	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr7:39649000-39649600	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr7:39649000-39649600	Active TSS	Fetal Kidney	kidney
30	chr7:39649000-39649600	Flanking Active TSS	Fetal Lung	lung
31	chr7:39649000-39649600	Enhancers	Fetal Muscle Trunk	muscle
32	chr7:39649000-39649800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
33	chr7:39649000-39649800	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr7:39649000-39649800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr7:39649000-39649800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr7:39649000-39649800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr7:39649000-39649800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr7:39649000-39649800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr7:39649000-39649800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr7:39649000-39649800	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr7:39649000-39649800	Enhancers	Fetal Heart	heart
42	chr7:39649000-39649800	Active TSS	Rectal Smooth Muscle	rectum
43	chr7:39649000-39649800	Active TSS	Right Atrium	heart
44	chr7:39649000-39649800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
45	chr7:39649000-39649800	Flanking Active TSS	NHDF-Ad	bronchial
46	chr7:39649000-39650000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
47	chr7:39649000-39650000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr7:39649000-39650000	Flanking Active TSS	NHEK	skin
49	chr7:39649200-39649600	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr7:39649200-39649600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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