Variant report

Variant	rs3803088
Chromosome Location	chr12:117150050-117150051
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	chr12:117147973..117150592-chr12:117175280..117177102,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNFT2-1	chr12:117149742-117150681	ENSG00000250553
2	lnc-C12orf49-3	chr12:117149738-117150681	NONHSAT030961
3	lnc-RNFT2-1	chr12:117150040-117150385	NONHSAT030958

Variant related genes	Relation type
ENSG00000111412	Chromatin interaction
ENSG00000135119	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs182889	0.80[EUR][1000 genomes]
rs339457	0.95[MEX][hapmap];0.80[EUR][1000 genomes]
rs339460	0.95[MEX][hapmap];0.81[EUR][1000 genomes]
rs429963	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.82[EUR][1000 genomes];0.81[ASN][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	nsv832523	chr12:117090343-117273810	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3803088	SRRM4	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117146200-117152000	Weak transcription	Spleen	Spleen
2	chr12:117147200-117150200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:117147200-117153000	Weak transcription	Left Ventricle	heart
4	chr12:117147200-117153000	Weak transcription	HepG2	liver
5	chr12:117147200-117153400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr12:117147200-117153800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:117147200-117155200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:117147200-117155400	Weak transcription	Right Atrium	heart
9	chr12:117147200-117155800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr12:117147200-117155800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr12:117147200-117156400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:117147200-117174000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr12:117147400-117150200	Weak transcription	Gastric	stomach
14	chr12:117147400-117150200	Weak transcription	GM12878-XiMat	blood
15	chr12:117147400-117151000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr12:117147400-117151600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:117147400-117151800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr12:117147400-117151800	Weak transcription	Pancreas	Pancrea
19	chr12:117147400-117152000	Weak transcription	Dnd41	blood
20	chr12:117147400-117152800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr12:117147400-117153000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr12:117147400-117153200	Weak transcription	Primary B cells from cord blood	blood
23	chr12:117147400-117153200	Weak transcription	Aorta	Aorta
24	chr12:117147400-117153400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr12:117147400-117153400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr12:117147400-117153400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:117147400-117153800	Weak transcription	Ovary	ovary
28	chr12:117147400-117154200	Weak transcription	Colonic Mucosa	Colon
29	chr12:117147400-117155400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr12:117147400-117155800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:117147400-117156000	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:117147400-117156000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr12:117147400-117157000	Weak transcription	Right Ventricle	heart
34	chr12:117147400-117158000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr12:117147400-117173600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:117147600-117150200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:117147600-117150200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:117147600-117151600	Weak transcription	NHDF-Ad	bronchial
39	chr12:117147600-117152400	Weak transcription	Primary B cells from peripheral blood	blood
40	chr12:117147600-117152800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:117147600-117153200	Weak transcription	Hela-S3	cervix
42	chr12:117147800-117151200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:117147800-117151200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr12:117147800-117153600	Weak transcription	A549	lung
45	chr12:117148000-117152000	Weak transcription	Fetal Intestine Large	intestine
46	chr12:117148000-117153200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr12:117148200-117152000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr12:117148200-117154200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr12:117148400-117150400	Weak transcription	Brain Cingulate Gyrus	brain
50	chr12:117148400-117150400	Weak transcription	Brain Substantia Nigra	brain

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