Variant report

Variant	rs12824925
Chromosome Location	chr12:122802641-122802642
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122792061..122794415-chr12:122801391..122803054,2	K562	blood:
2	chr12:122797956..122799865-chr12:122801211..122803514,2	K562	blood:
3	chr12:122800426..122802982-chr12:122821173..122823608,2	K562	blood:
4	chr12:122795079..122797020-chr12:122799854..122802768,2	K562	blood:
5	chr12:122800426..122803308-chr12:122822108..122823618,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10270	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs10848035	0.81[EUR][1000 genomes]
rs11060167	0.95[CEU][hapmap]
rs11060333	0.95[CEU][hapmap]
rs12423987	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12424872	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs12425684	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12578739	0.83[EUR][1000 genomes]
rs12578815	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs12578863	0.84[EUR][1000 genomes]
rs12578953	0.86[ASN][1000 genomes]
rs12580084	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs12809220	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12810587	0.91[CEU][hapmap]
rs12811503	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12814516	0.83[EUR][1000 genomes]
rs12814554	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12814923	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12816400	0.81[EUR][1000 genomes]
rs12816499	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs12820704	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs12822121	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12824385	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12824701	0.91[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12825008	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12825149	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12825279	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12826834	0.84[EUR][1000 genomes]
rs12831210	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1512023	1.00[ASW][hapmap];0.91[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];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2063510	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs2068223	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2271408	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[EUR][1000 genomes]
rs2271409	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2277332	0.90[JPT][hapmap]
rs2277333	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34383196	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35030971	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35772530	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35963777	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3782153	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3782154	0.90[JPT][hapmap]
rs3809116	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs4567503	0.90[JPT][hapmap]
rs4758649	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4758650	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs4758670	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs4758677	0.95[CEU][hapmap]
rs6488906	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6488909	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7313284	1.00[YRI][hapmap]
rs7388	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7962385	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs7963565	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs7970027	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs872451	0.91[CEU][hapmap]
rs907482	0.83[CEU][hapmap];0.90[JPT][hapmap]

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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12824925	IL31	cis	parietal	SCAN
rs12824925	VPS33A	cis	lymphoblastoid	seeQTL
rs12824925	GPR109A	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122751600-122803400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:122752400-122810400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr12:122754600-122822400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr12:122763600-122812000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:122765800-122803400	Weak transcription	K562	blood
6	chr12:122770200-122821600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr12:122770400-122821800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:122775600-122833600	Strong transcription	Liver	Liver
9	chr12:122776000-122822200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:122778000-122808800	Weak transcription	Fetal Heart	heart
11	chr12:122780000-122827200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:122780400-122812000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:122780400-122812600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:122781400-122821400	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:122782800-122803400	Weak transcription	Colonic Mucosa	Colon
16	chr12:122782800-122803800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr12:122785800-122827200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:122786200-122803200	Strong transcription	Stomach Smooth Muscle	stomach
19	chr12:122787000-122803800	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:122787200-122809000	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr12:122787400-122803600	Weak transcription	Stomach Mucosa	stomach
22	chr12:122787800-122804400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:122788200-122821200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr12:122790000-122810800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:122791200-122841600	Strong transcription	Placenta	Placenta
26	chr12:122792400-122819800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:122793400-122810600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr12:122794600-122811800	Weak transcription	Small Intestine	intestine
29	chr12:122794600-122832600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:122795400-122803000	Strong transcription	Adipose Nuclei	Adipose
31	chr12:122795600-122810600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:122795800-122818200	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr12:122796000-122802800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:122796200-122803400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr12:122796200-122808600	Strong transcription	Fetal Muscle Trunk	muscle
36	chr12:122796400-122804000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:122796600-122804000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:122796800-122804200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr12:122796800-122808600	Strong transcription	Fetal Stomach	stomach
40	chr12:122797000-122803800	Strong transcription	Lung	lung
41	chr12:122797000-122808800	Strong transcription	Fetal Intestine Small	intestine
42	chr12:122797200-122805200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr12:122797200-122814000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:122797200-122822400	Strong transcription	Fetal Muscle Leg	muscle
45	chr12:122797400-122803400	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:122797400-122804200	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr12:122797400-122808600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:122797600-122803600	Strong transcription	Duodenum Mucosa	Duodenum
49	chr12:122797600-122804200	Strong transcription	Fetal Brain Female	brain
50	chr12:122797600-122804800	Strong transcription	Primary T helper cells fromperipheralblood	blood

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