Variant report

Variant	rs78629091
Chromosome Location	chr7:66809439-66809440
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:66806712..66809740-chr7:66809964..66812550,3	K562	blood:
2	chr7:66808425..66811415-chr7:66821937..66824541,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STAG3L4-1	chr7:66809042-66809767	NONHSAT121283

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv888330	chr7:66502171-66877880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
4	nsv1027702	chr7:66722103-66841913	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv1031048	chr7:66722103-66844039	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv966839	chr7:66805198-66815088	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1031560	chr7:66805244-66846663	Enhancers Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1022779	chr7:66805244-66849392	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv970413	chr7:66808251-66815088	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs78629091	STAG3L4	cis	Artery Tibial	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66781400-66810200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr7:66785800-66816200	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr7:66801200-66812000	Weak transcription	Gastric	stomach
4	chr7:66802600-66809600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr7:66802600-66811800	Weak transcription	Stomach Mucosa	stomach
6	chr7:66802800-66814800	Weak transcription	HSMMtube	muscle
7	chr7:66803200-66811600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr7:66804400-66809800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:66804400-66810000	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr7:66804400-66810200	Strong transcription	Fetal Intestine Large	intestine
11	chr7:66804600-66809800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
12	chr7:66804600-66810400	Strong transcription	Primary T cells from cord blood	blood
13	chr7:66804600-66811200	Strong transcription	Duodenum Mucosa	Duodenum
14	chr7:66804800-66809600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr7:66805200-66809600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr7:66805200-66816200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr7:66806200-66813400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr7:66806400-66809600	Weak transcription	Brain Substantia Nigra	brain
19	chr7:66806600-66809600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr7:66806600-66810000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr7:66807200-66809600	Weak transcription	Brain Angular Gyrus	brain
22	chr7:66807200-66809600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr7:66807200-66811000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr7:66807200-66819600	Weak transcription	Brain Anterior Caudate	brain
25	chr7:66807200-66822400	Weak transcription	Brain Hippocampus Middle	brain
26	chr7:66807800-66809600	Genic enhancers	Fetal Muscle Leg	muscle
27	chr7:66808000-66809600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr7:66808000-66809600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr7:66808000-66810200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
30	chr7:66808200-66810200	Strong transcription	Primary B cells from cord blood	blood
31	chr7:66808200-66810600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr7:66808400-66810000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
33	chr7:66808400-66810200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr7:66808400-66816200	Weak transcription	Thymus	Thymus
35	chr7:66808400-66822200	Weak transcription	Right Ventricle	heart
36	chr7:66808600-66809800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr7:66808600-66810000	ZNF genes & repeats	Aorta	Aorta
38	chr7:66808600-66810200	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr7:66808800-66810000	Genic enhancers	Psoas Muscle	Psoas
40	chr7:66808800-66815600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr7:66809000-66809600	Weak transcription	Fetal Brain Female	brain
42	chr7:66809000-66809600	Weak transcription	Left Ventricle	heart
43	chr7:66809000-66810000	Strong transcription	Colon Smooth Muscle	Colon
44	chr7:66809000-66810400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr7:66809000-66810400	ZNF genes & repeats	NHEK	skin
46	chr7:66809000-66810600	ZNF genes & repeats	Fetal Stomach	stomach
47	chr7:66809000-66812400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
48	chr7:66809200-66809600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr7:66809200-66809800	ZNF genes & repeats	Esophagus	oesophagus
50	chr7:66809200-66810000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links