Variant report

Variant	rs2730653
Chromosome Location	chr12:51548623-51548624
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	chr12:51546648..51549311-chr12:51552488..51556215,3	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10876133	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10876135	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[ASN][1000 genomes]
rs10876137	0.90[ASN][1000 genomes]
rs10876141	0.88[ASN][1000 genomes]
rs10876142	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10876150	0.81[ASN][1000 genomes]
rs11169643	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs11169658	0.83[CHB][hapmap]
rs11169696	1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.81[MEX][hapmap];0.85[ASN][1000 genomes]
rs11169700	0.87[ASN][1000 genomes]
rs11169706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169720	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169721	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169722	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169733	0.83[ASN][1000 genomes]
rs11169734	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11169735	0.89[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11169737	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169741	0.81[ASN][1000 genomes]
rs11169746	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11169747	0.94[JPT][hapmap]
rs11614806	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12227032	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12227734	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs12227973	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12230388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12312531	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12424460	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs1493382	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17125363	0.87[ASN][1000 genomes]
rs17125365	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17125371	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2269683	0.81[TSI][hapmap]
rs2359189	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2436636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2452793	0.85[ASN][1000 genomes]
rs2452794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2452795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2452796	0.99[ASN][1000 genomes]
rs2640509	0.80[ASN][1000 genomes]
rs2640512	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2640515	0.99[ASN][1000 genomes]
rs2640518	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2640520	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2640522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2640525	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2640526	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2640528	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2730651	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2730657	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2730659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2730660	0.84[ASN][1000 genomes]
rs28392616	0.81[ASN][1000 genomes]
rs2934092	0.94[ASN][1000 genomes]
rs2956427	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2956433	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4768953	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4768957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs4768971	0.99[ASN][1000 genomes]
rs4768974	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56729853	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60203224	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7309374	0.99[ASN][1000 genomes]
rs7399208	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7399214	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953765	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7965004	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7980076	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8490	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2730653	TFCP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51477800-51550200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:51503200-51560200	Weak transcription	Right Ventricle	heart
3	chr12:51504800-51563400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:51510200-51554400	Weak transcription	K562	blood
5	chr12:51511400-51558800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr12:51513000-51565400	Weak transcription	Fetal Lung	lung
7	chr12:51517200-51554600	Weak transcription	HepG2	liver
8	chr12:51519000-51561600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:51519000-51565000	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:51519000-51565200	Weak transcription	Left Ventricle	heart
11	chr12:51519000-51565200	Weak transcription	Pancreas	Pancrea
12	chr12:51519000-51565800	Weak transcription	Esophagus	oesophagus
13	chr12:51519200-51554600	Weak transcription	NHDF-Ad	bronchial
14	chr12:51519200-51559600	Weak transcription	Lung	lung
15	chr12:51519200-51563800	Weak transcription	Fetal Brain Female	brain
16	chr12:51519200-51565000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr12:51519400-51550200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:51519400-51565200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:51521600-51565200	Weak transcription	HSMM	muscle
20	chr12:51526000-51558800	Weak transcription	GM12878-XiMat	blood
21	chr12:51526800-51556400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:51527400-51565200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:51528200-51554600	Weak transcription	A549	lung
24	chr12:51530600-51564200	Weak transcription	Fetal Muscle Leg	muscle
25	chr12:51531200-51563400	Weak transcription	Hela-S3	cervix
26	chr12:51531800-51550200	Weak transcription	NHEK	skin
27	chr12:51531800-51554400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:51532000-51565000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr12:51532200-51550000	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr12:51532400-51564000	Weak transcription	Primary T cells from cord blood	blood
31	chr12:51532600-51554400	Weak transcription	Brain Angular Gyrus	brain
32	chr12:51532600-51562000	Weak transcription	Ovary	ovary
33	chr12:51532600-51562800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr12:51532600-51564800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr12:51532600-51565200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr12:51532800-51563600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:51533000-51554600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:51533000-51563200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:51533200-51555800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:51533200-51561400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:51533200-51561400	Weak transcription	Placenta	Placenta
42	chr12:51533200-51564800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:51533400-51553600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr12:51533400-51560200	Weak transcription	Dnd41	blood
45	chr12:51533600-51564800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr12:51533600-51565000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:51534600-51564200	Weak transcription	Fetal Intestine Large	intestine
48	chr12:51537000-51550200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:51538600-51554200	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr12:51539600-51565000	Weak transcription	Primary B cells from peripheral blood	blood

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