Variant report

Variant	rs10774514
Chromosome Location	chr12:120242845-120242846
allele	A/G
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	CTCF	chr12:120241693-120242868	SK-N-SH	brain:	n/a	n/a
2	MXI1	chr12:120241035-120243037	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:120208689..120211170-chr12:120242508..120245374,3	MCF-7	breast:

Variant related genes	Relation type
CIT	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10744743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10774515	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs10774516	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs10849699	0.89[CHB][hapmap]
rs11064910	0.90[CHB][hapmap];0.86[CHD][hapmap]
rs11064913	0.89[CHB][hapmap]
rs11064915	0.90[CHB][hapmap]
rs1182807	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs12231774	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs203336	0.89[EUR][1000 genomes]
rs203340	0.87[CEU][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs203356	0.89[EUR][1000 genomes]
rs2107661	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs280581	0.90[CHB][hapmap]
rs280582	0.95[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs280588	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs280589	0.84[EUR][1000 genomes]
rs372803	0.89[EUR][1000 genomes]
rs377876	0.95[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3809307	0.90[CHB][hapmap]
rs3847959	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3847960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs430998	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs435136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs450902	0.95[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs473430	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767848	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4767849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6490270	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7294469	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308076	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs740032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7975107	0.80[CHB][hapmap]
rs7978181	0.89[CHB][hapmap]
rs804709	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10774514	PXN	cis	cerebellum	SCAN
rs10774514	SRRM4	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120190000-120244800	Weak transcription	Primary B cells from cord blood	blood
2	chr12:120209400-120293600	Weak transcription	Primary T cells from cord blood	blood
3	chr12:120223000-120255800	Weak transcription	HepG2	liver
4	chr12:120223000-120314400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:120229400-120256600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:120231000-120244800	Strong transcription	Dnd41	blood
7	chr12:120231200-120243800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr12:120232000-120246000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:120235000-120243600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:120235800-120244600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:120237200-120246400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:120237400-120250600	Weak transcription	Hela-S3	cervix
13	chr12:120240400-120244600	Weak transcription	GM12878-XiMat	blood
14	chr12:120241600-120276600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:120242000-120243400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:120242000-120244800	Weak transcription	K562	blood
17	chr12:120242200-120243000	Enhancers	Fetal Brain Male	brain
18	chr12:120242200-120243400	Genic enhancers	A549	lung
19	chr12:120242200-120244800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:120242400-120243200	Enhancers	HMEC	breast
21	chr12:120242400-120244600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:120242400-120244600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:120242400-120244800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr12:120242400-120245400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:120242600-120243000	Enhancers	Muscle Satellite Cultured Cells	--
26	chr12:120242600-120243200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:120242600-120243400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:120242600-120243400	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr12:120242600-120244600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:120242600-120244800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr12:120242600-120244800	Weak transcription	Fetal Muscle Leg	muscle
32	chr12:120242600-120246000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:120242600-120246400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr12:120242600-120246600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:120242600-120247400	Weak transcription	Thymus	Thymus
36	chr12:120242600-120247600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr12:120242600-120254200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr12:120242600-120259800	Weak transcription	NH-A	brain
39	chr12:120242600-120260200	Weak transcription	HUVEC	blood vessel
40	chr12:120242600-120276600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:120242600-120276800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr12:120242600-120279000	Weak transcription	Fetal Intestine Small	intestine
43	chr12:120242600-120279400	Weak transcription	Fetal Intestine Large	intestine
44	chr12:120242600-120293800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:120242600-120294400	Weak transcription	Fetal Kidney	kidney
46	chr12:120242800-120243000	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr12:120242800-120243000	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr12:120242800-120243000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr12:120242800-120243000	Enhancers	Brain Hippocampus Middle	brain
50	chr12:120242800-120243200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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