Variant report

Variant	rs13228079
Chromosome Location	chr7:30599408-30599409
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:30597466..30600428-chr7:30606686..30608995,2	K562	blood:
2	chr7:30587110..30590084-chr7:30597129..30599862,2	MCF-7	breast:
3	chr7:30591244..30593759-chr7:30599116..30600908,2	MCF-7	breast:
4	chr7:30595663..30599818-chr7:30601327..30605437,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GGCT-1	chr7:30587973-30601744	ENSG00000196295.7

Variant related genes	Relation type
ENSG00000263683	Chromatin interaction
ENSG00000196295	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10237725	0.86[JPT][hapmap]
rs10265589	0.82[JPT][hapmap]
rs10951271	0.96[CEU][hapmap];0.81[CHB][hapmap]

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	nsv538811	chr7:30549595-31405593	Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13228079	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs13228079	LOC222159	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30561600-30606400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr7:30563000-30599800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:30564400-30612200	Weak transcription	Colon Smooth Muscle	Colon
4	chr7:30569000-30602600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr7:30574800-30601000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr7:30575600-30600000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr7:30578200-30601200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr7:30586200-30601400	Weak transcription	Gastric	stomach
9	chr7:30586600-30620400	Weak transcription	Fetal Thymus	thymus
10	chr7:30587200-30602400	Weak transcription	Ovary	ovary
11	chr7:30590000-30600400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr7:30590200-30602600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr7:30591000-30601400	Weak transcription	Colonic Mucosa	Colon
14	chr7:30591200-30599800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr7:30591200-30600200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:30591200-30600200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr7:30591200-30600200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr7:30591200-30600200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr7:30591200-30600200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr7:30591200-30600400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr7:30591200-30600400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr7:30591200-30601000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr7:30591200-30601000	Weak transcription	Pancreas	Pancrea
24	chr7:30591200-30602000	Weak transcription	Right Atrium	heart
25	chr7:30591200-30602600	Weak transcription	Right Ventricle	heart
26	chr7:30591200-30602600	Weak transcription	Thymus	Thymus
27	chr7:30591200-30602800	Weak transcription	Osteobl	bone
28	chr7:30591200-30604000	Weak transcription	Stomach Mucosa	stomach
29	chr7:30591200-30606200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr7:30591200-30610200	Weak transcription	Small Intestine	intestine
31	chr7:30591200-30612400	Weak transcription	Brain Germinal Matrix	brain
32	chr7:30591200-30633400	Weak transcription	Psoas Muscle	Psoas
33	chr7:30591400-30603000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr7:30591400-30603000	Weak transcription	A549	lung
35	chr7:30591800-30600600	Weak transcription	NHDF-Ad	bronchial
36	chr7:30591800-30600800	Weak transcription	NHLF	lung
37	chr7:30591800-30601000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr7:30592000-30601000	Weak transcription	Hela-S3	cervix
39	chr7:30592600-30602600	Weak transcription	HepG2	liver
40	chr7:30593000-30606600	Weak transcription	Fetal Kidney	kidney
41	chr7:30593400-30600200	Weak transcription	Primary B cells from cord blood	blood
42	chr7:30593800-30609400	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr7:30595400-30599600	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr7:30595600-30609000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr7:30595800-30608600	Strong transcription	Placenta	Placenta
46	chr7:30595800-30608800	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr7:30596200-30602000	Strong transcription	Fetal Stomach	stomach
48	chr7:30596200-30607200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr7:30596200-30608200	Strong transcription	Fetal Intestine Small	intestine
50	chr7:30596400-30603600	Strong transcription	Liver	Liver

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