Variant report

Variant	rs559583993
Chromosome Location	chr7:5460251-5460252
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:5458614..5460773-chr7:5569317..5571189,3	K562	blood:
2	chr7:5458987..5464555-chr7:5593156..5597256,5	K562	blood:
3	chr7:5458325..5469295-chr7:5567159..5574053,21	MCF-7	breast:
4	chr7:5458325..5461852-chr7:5568883..5572530,6	MCF-7	breast:
5	chr7:5459451..5462326-chr7:5602186..5603926,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC29A4-1	chr7:5459967-5460398	ENSG00000241269.1

Variant related genes	Relation type
ENSG00000075624	Chromatin interaction
ENSG00000272719	Chromatin interaction
ENSG00000263900	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
2	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
3	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
4	nsv887391	chr7:5224407-5572132	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	292 gene(s)	inside rSNPs	diseases
5	nsv823996	chr7:5285503-5465988	Flanking Active TSS Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv887396	chr7:5305297-5475409	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	esv1814049	chr7:5314993-5675131	Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer 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 miRNA target site	333 gene(s)	inside rSNPs	diseases
8	esv1820266	chr7:5332088-5665173	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
9	nsv533965	chr7:5370746-5548397	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
10	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
11	nsv887401	chr7:5393243-5539958	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
12	nsv887402	chr7:5394951-5494677	Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	nsv887404	chr7:5402606-5667645	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	331 gene(s)	inside rSNPs	diseases
14	nsv887405	chr7:5409059-5552436	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
15	nsv887406	chr7:5414602-5552436	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
16	nsv916391	chr7:5417945-5889565	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	336 gene(s)	inside rSNPs	diseases
17	nsv887407	chr7:5432672-5605130	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	302 gene(s)	inside rSNPs	diseases
18	nsv887408	chr7:5432672-5667645	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	331 gene(s)	inside rSNPs	diseases
19	nsv508443	chr7:5447283-5501122	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
20	nsv526194	chr7:5452756-5592436	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	278 gene(s)	inside rSNPs	diseases
21	nsv823997	chr7:5457916-5463961	Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
22	esv3428734	chr7:5458676-5468674	Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
23	esv3373616	chr7:5459851-5462399	Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5457000-5461400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:5457200-5461000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
3	chr7:5457600-5461000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:5457800-5461400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr7:5458000-5460400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
6	chr7:5458000-5461000	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr7:5458000-5461200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
8	chr7:5458000-5461600	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
9	chr7:5458200-5460800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
10	chr7:5458200-5460800	Transcr. at gene 5' and 3'	Fetal Lung	lung
11	chr7:5458400-5460400	Bivalent/Poised TSS	Thymus	Thymus
12	chr7:5458400-5461000	Transcr. at gene 5' and 3'	NHLF	lung
13	chr7:5458400-5462800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr7:5458400-5462800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
15	chr7:5458400-5469800	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr7:5458600-5460600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
17	chr7:5458600-5460800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
18	chr7:5458600-5460800	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr7:5458600-5460800	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
20	chr7:5458600-5468200	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr7:5458600-5469400	Active TSS	Aorta	Aorta
22	chr7:5458600-5469400	Active TSS	Psoas Muscle	Psoas
23	chr7:5458600-5469800	Active TSS	Fetal Kidney	kidney
24	chr7:5458800-5462800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
25	chr7:5458800-5462800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr7:5458800-5462800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
27	chr7:5458800-5467000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr7:5458800-5468000	Active TSS	Brain Angular Gyrus	brain
29	chr7:5458800-5469400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr7:5458800-5469400	Active TSS	NHDF-Ad	bronchial
31	chr7:5458800-5469600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:5458800-5469600	Active TSS	Colon Smooth Muscle	Colon
33	chr7:5458800-5469800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr7:5458800-5470000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr7:5458800-5470000	Active TSS	HSMMtube	muscle
36	chr7:5459000-5460600	Active TSS	Sigmoid Colon	Sigmoid Colon
37	chr7:5459000-5461000	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
38	chr7:5459000-5461000	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
39	chr7:5459000-5463800	Active TSS	Right Atrium	heart
40	chr7:5459000-5467000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr7:5459000-5467800	Active TSS	Brain Cingulate Gyrus	brain
42	chr7:5459000-5468000	Active TSS	Brain Substantia Nigra	brain
43	chr7:5459000-5468200	Active TSS	HSMM	muscle
44	chr7:5459000-5468400	Active TSS	Left Ventricle	heart
45	chr7:5459000-5468800	Active TSS	Fetal Intestine Large	intestine
46	chr7:5459000-5468800	Active TSS	Rectal Smooth Muscle	rectum
47	chr7:5459000-5469400	Active TSS	Gastric	stomach
48	chr7:5459000-5469400	Active TSS	Small Intestine	intestine
49	chr7:5459000-5469600	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr7:5459000-5469800	Active TSS	Ovary	ovary

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