Variant report

Variant	rs3784553
Chromosome Location	chr15:56972217-56972218
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56965225..56966905-chr15:56971414..56973498,2	MCF-7	breast:
2	chr15:56967231..56970403-chr15:56971950..56973843,3	K562	blood:

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

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10518871	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11852822	0.87[ASN][1000 genomes]
rs12912666	0.80[CHB][hapmap]
rs16977020	0.90[CEU][hapmap];0.81[CHB][hapmap];0.82[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs2046213	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2128171	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs59066195	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6493882	0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[ASN][1000 genomes]
rs7164095	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];0.91[ASN][1000 genomes]
rs7165211	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7171500	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7172110	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7179781	0.86[EUR][1000 genomes]
rs7181745	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72744938	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[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	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3784553	TCF12	cis	lymphoblastoid	seeQTL
rs3784553	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56916600-56990800	Weak transcription	Pancreas	Pancrea
2	chr15:56917800-56990600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:56917800-56990600	Weak transcription	NHLF	lung
4	chr15:56919800-57016600	Weak transcription	Small Intestine	intestine
5	chr15:56924000-56990600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:56924000-56990800	Weak transcription	NHEK	skin
7	chr15:56928400-56996800	Weak transcription	Gastric	stomach
8	chr15:56937400-57000200	Weak transcription	Colonic Mucosa	Colon
9	chr15:56939200-56990800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:56939400-56986000	Weak transcription	Brain Substantia Nigra	brain
11	chr15:56945800-56990800	Weak transcription	Fetal Brain Male	brain
12	chr15:56946000-56990800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr15:56946200-56990800	Weak transcription	Right Ventricle	heart
14	chr15:56955800-56990600	Weak transcription	Esophagus	oesophagus
15	chr15:56956000-56973400	Weak transcription	Aorta	Aorta
16	chr15:56957400-56975600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr15:56958000-56990200	Weak transcription	A549	lung
18	chr15:56958200-56990200	Weak transcription	Fetal Muscle Leg	muscle
19	chr15:56958400-56990600	Weak transcription	Lung	lung
20	chr15:56958400-56990800	Weak transcription	Brain Germinal Matrix	brain
21	chr15:56958400-57019200	Weak transcription	Fetal Intestine Small	intestine
22	chr15:56958600-56990600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:56959200-56990400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:56959200-56990600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr15:56959200-56990600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:56959200-56990600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr15:56959200-56992000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:56959400-56986000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:56960800-56992000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr15:56961200-56990600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr15:56961200-56992200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr15:56965200-56973600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr15:56965600-56990800	Weak transcription	K562	blood
34	chr15:56966800-56973600	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr15:56967000-56990800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:56967600-56990600	Weak transcription	Left Ventricle	heart
37	chr15:56968200-56976000	Weak transcription	Colon Smooth Muscle	Colon
38	chr15:56968400-56990600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:56968400-56992000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr15:56968400-56992000	Weak transcription	HSMMtube	muscle
41	chr15:56968600-56990000	Weak transcription	NH-A	brain
42	chr15:56968800-56976000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr15:56968800-56976000	Weak transcription	Fetal Heart	heart
44	chr15:56968800-56990000	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr15:56968800-56990200	Weak transcription	Osteobl	bone
46	chr15:56969000-56990800	Weak transcription	HMEC	breast
47	chr15:56969200-56979800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr15:56969400-56976000	Weak transcription	Brain Hippocampus Middle	brain
49	chr15:56969400-56990200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr15:56969400-56990400	Weak transcription	Rectal Mucosa Donor 29	rectum

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