Variant report

Variant	rs1274496
Chromosome Location	chr12:56625693-56625694
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56625630-56625886	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56510236..56513593-chr12:56624409..56626987,3	K562	blood:
2	chr12:56623929..56626339-chr12:56638074..56640229,2	MCF-7	breast:

Variant related genes	Relation type
SLC39A5	TF binding region
ENSG00000229117	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000139645	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1274490	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1295772	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17118403	0.86[EUR][1000 genomes]
rs17118409	0.82[EUR][1000 genomes]
rs17118431	0.81[EUR][1000 genomes]
rs2629452	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35526714	0.82[EUR][1000 genomes]
rs57343616	0.84[EUR][1000 genomes]
rs59626664	0.82[EUR][1000 genomes]
rs59822547	0.82[EUR][1000 genomes]
rs60913149	0.82[EUR][1000 genomes]
rs808919	0.83[AMR][1000 genomes]
rs901073	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1274496	RP11-977G19.11	cis	Artery Tibial	GTEx
rs1274496	TMEM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56618600-56633800	Weak transcription	Aorta	Aorta
2	chr12:56618800-56628200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:56618800-56628600	Weak transcription	Esophagus	oesophagus
4	chr12:56618800-56629800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:56618800-56629800	Weak transcription	Primary T cells from cord blood	blood
6	chr12:56618800-56630200	Weak transcription	Ovary	ovary
7	chr12:56618800-56630400	Weak transcription	Fetal Thymus	thymus
8	chr12:56618800-56631200	Weak transcription	HSMMtube	muscle
9	chr12:56618800-56633000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr12:56618800-56633000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr12:56618800-56634600	Weak transcription	Psoas Muscle	Psoas
12	chr12:56618800-56635200	Weak transcription	Small Intestine	intestine
13	chr12:56618800-56635400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:56618800-56637800	Weak transcription	Fetal Kidney	kidney
15	chr12:56619000-56630400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:56619000-56631000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr12:56619000-56632000	Weak transcription	Colon Smooth Muscle	Colon
18	chr12:56619000-56633000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:56619000-56633200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:56619000-56633400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr12:56619000-56633600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr12:56619000-56634000	Weak transcription	Primary B cells from cord blood	blood
23	chr12:56619000-56634800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:56619200-56626800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr12:56619200-56628600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr12:56619200-56630000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr12:56619200-56630400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:56619200-56631000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr12:56619200-56631200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr12:56619200-56631400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr12:56619200-56632400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr12:56619200-56633000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:56619200-56633000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr12:56619200-56633000	Weak transcription	Left Ventricle	heart
35	chr12:56619200-56633400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:56619200-56633400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:56619200-56634400	Weak transcription	Fetal Lung	lung
38	chr12:56619200-56634600	Weak transcription	HUVEC	blood vessel
39	chr12:56619200-56635000	Weak transcription	HSMM	muscle
40	chr12:56619200-56635400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr12:56619200-56637600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:56619400-56629200	Weak transcription	Brain Germinal Matrix	brain
43	chr12:56619400-56629800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr12:56619400-56629800	Weak transcription	Osteobl	bone
45	chr12:56619400-56630000	Weak transcription	A549	lung
46	chr12:56619400-56632600	Weak transcription	NHDF-Ad	bronchial
47	chr12:56619400-56634600	Weak transcription	NH-A	brain
48	chr12:56619400-56637200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr12:56619400-56637800	Weak transcription	Right Atrium	heart
50	chr12:56619600-56629800	Weak transcription	Muscle Satellite Cultured Cells	--

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