Variant report

Variant	rs7939005
Chromosome Location	chr11:77443627-77443628
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11237260	1.00[YRI][hapmap]
rs11237300	0.85[LWK][hapmap];1.00[YRI][hapmap]
rs11827910	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs17825097	0.85[LWK][hapmap];1.00[YRI][hapmap]
rs7107540	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs7112260	1.00[AMR][1000 genomes]
rs728130	0.85[LWK][hapmap];1.00[YRI][hapmap]
rs7930079	1.00[AMR][1000 genomes]
rs7930581	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1050891	chr11:77416645-77788002	Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1037292	chr11:77431583-77745934	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv541092	chr11:77431583-77745934	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv975951	chr11:77440719-77446428	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7939005	SEMA5A	trans	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77394600-77445600	Weak transcription	Esophagus	oesophagus
2	chr11:77394600-77458800	Weak transcription	Small Intestine	intestine
3	chr11:77394800-77462600	Weak transcription	Fetal Heart	heart
4	chr11:77407200-77448000	Weak transcription	K562	blood
5	chr11:77409600-77453400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr11:77409600-77458800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr11:77409600-77478200	Weak transcription	Brain Angular Gyrus	brain
8	chr11:77410400-77477600	Weak transcription	Brain Substantia Nigra	brain
9	chr11:77431600-77482400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr11:77436200-77445400	Weak transcription	NHLF	lung
11	chr11:77436200-77445600	Weak transcription	Gastric	stomach
12	chr11:77436200-77451400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr11:77436200-77458600	Weak transcription	HSMMtube	muscle
14	chr11:77436200-77462600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr11:77436200-77463000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr11:77436200-77473400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr11:77436200-77477000	Weak transcription	Colonic Mucosa	Colon
18	chr11:77436400-77444400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr11:77436600-77444600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr11:77436600-77450200	Weak transcription	HSMM	muscle
21	chr11:77436600-77473200	Weak transcription	NHDF-Ad	bronchial
22	chr11:77436800-77458600	Weak transcription	NH-A	brain
23	chr11:77441400-77443800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
24	chr11:77441400-77443800	ZNF genes & repeats	GM12878-XiMat	blood
25	chr11:77441400-77444400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr11:77441400-77445000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:77441400-77452000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr11:77441600-77443800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
29	chr11:77441600-77443800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:77441600-77443800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:77441600-77443800	ZNF genes & repeats	Fetal Intestine Small	intestine
32	chr11:77441600-77444000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
33	chr11:77441600-77444000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr11:77441600-77444200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:77441600-77445200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
36	chr11:77441800-77443800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
37	chr11:77441800-77443800	ZNF genes & repeats	Primary T cells from cord blood	blood
38	chr11:77441800-77443800	ZNF genes & repeats	Brain Germinal Matrix	brain
39	chr11:77441800-77443800	ZNF genes & repeats	Thymus	Thymus
40	chr11:77441800-77444600	ZNF genes & repeats	Dnd41	blood
41	chr11:77441800-77445000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
42	chr11:77442000-77453000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr11:77442200-77443800	ZNF genes & repeats	Fetal Stomach	stomach
44	chr11:77442200-77444000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
45	chr11:77442200-77444800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr11:77442200-77446200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr11:77442200-77451800	Weak transcription	Fetal Brain Male	brain
48	chr11:77442400-77444000	Strong transcription	Fetal Lung	lung
49	chr11:77442400-77444800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr11:77442400-77444800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links