Variant report

Variant	rs2730647
Chromosome Location	chr12:51554826-51554827
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr12:51554816-51555056	K562	blood:	n/a	n/a
2	ZMIZ1	chr12:51554727-51554959	K562	blood:	n/a	n/a
3	MAFK	chr12:51554819-51555043	K562	blood:	n/a	n/a
4	FOXA1	chr12:51554756-51555232	HepG2	liver:	n/a	n/a
5	EP300	chr12:51554772-51555232	HepG2	liver:	n/a	n/a
6	CBX3	chr12:51554769-51555115	K562	blood:	n/a	n/a
7	FOXA1	chr12:51554805-51555245	HepG2	liver:	n/a	n/a
8	TEAD4	chr12:51554755-51555254	HepG2	liver:	n/a	n/a
9	MAFF	chr12:51554811-51555099	K562	blood:	n/a	n/a
10	TEAD4	chr12:51554719-51555146	K562	blood:	n/a	n/a
11	RCOR1	chr12:51554808-51555131	K562	blood:	n/a	n/a
12	FOXA2	chr12:51554798-51555219	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51554796..51557300-chr12:51565911..51568570,2	K562	blood:
2	chr12:51554454..51555957-chr12:51556560..51559304,2	K562	blood:
3	chr12:51554796..51556370-chr12:51565911..51567778,2	K562	blood:
4	chr12:51546648..51549311-chr12:51552488..51556215,3	K562	blood:
5	chr12:51475915..51477479-chr12:51552231..51555145,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNU6-199P	TF binding region
ENSG00000200953	TF binding region
ENSG00000199824	Chromatin interaction
ENSG00000110925	Chromatin interaction
ENSG00000135457	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10783414	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783416	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10783417	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10783418	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10876143	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10876146	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11613085	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1565721	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1984544	0.93[ASN][1000 genomes]
rs1985457	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2029686	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2436645	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2436646	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2436647	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2640511	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2640516	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2640521	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2640523	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2640527	0.93[ASN][1000 genomes]
rs2730648	0.86[ASN][1000 genomes]
rs2730650	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2730654	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2956428	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3110188	0.82[ASN][1000 genomes]
rs6580799	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6580800	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6580801	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6580803	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6580804	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7306522	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7959378	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	esv2762980	chr12:51527963-51561056	Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51503200-51560200	Weak transcription	Right Ventricle	heart
2	chr12:51504800-51563400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr12:51511400-51558800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr12:51513000-51565400	Weak transcription	Fetal Lung	lung
5	chr12:51519000-51561600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:51519000-51565000	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:51519000-51565200	Weak transcription	Left Ventricle	heart
8	chr12:51519000-51565200	Weak transcription	Pancreas	Pancrea
9	chr12:51519000-51565800	Weak transcription	Esophagus	oesophagus
10	chr12:51519200-51559600	Weak transcription	Lung	lung
11	chr12:51519200-51563800	Weak transcription	Fetal Brain Female	brain
12	chr12:51519200-51565000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr12:51519400-51565200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:51521600-51565200	Weak transcription	HSMM	muscle
15	chr12:51526000-51558800	Weak transcription	GM12878-XiMat	blood
16	chr12:51526800-51556400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:51527400-51565200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:51530600-51564200	Weak transcription	Fetal Muscle Leg	muscle
19	chr12:51531200-51563400	Weak transcription	Hela-S3	cervix
20	chr12:51532000-51565000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr12:51532400-51564000	Weak transcription	Primary T cells from cord blood	blood
22	chr12:51532600-51562000	Weak transcription	Ovary	ovary
23	chr12:51532600-51562800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr12:51532600-51564800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr12:51532600-51565200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr12:51532800-51563600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:51533000-51563200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:51533200-51555800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr12:51533200-51561400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:51533200-51561400	Weak transcription	Placenta	Placenta
31	chr12:51533200-51564800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:51533400-51560200	Weak transcription	Dnd41	blood
33	chr12:51533600-51564800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr12:51533600-51565000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:51534600-51564200	Weak transcription	Fetal Intestine Large	intestine
36	chr12:51539600-51565000	Weak transcription	Primary B cells from peripheral blood	blood
37	chr12:51539800-51556800	Weak transcription	Fetal Stomach	stomach
38	chr12:51539800-51561000	Weak transcription	Aorta	Aorta
39	chr12:51540000-51560200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:51540200-51557600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr12:51540800-51557800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:51540800-51564800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr12:51541000-51560200	Weak transcription	Primary B cells from cord blood	blood
44	chr12:51543200-51565200	Weak transcription	Psoas Muscle	Psoas
45	chr12:51545000-51558800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr12:51545000-51564200	Weak transcription	Brain Germinal Matrix	brain
47	chr12:51545000-51565000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:51545000-51565000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr12:51549000-51557400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr12:51550200-51563200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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