Variant report

Variant	rs12065840
Chromosome Location	chr1:224833490-224833491
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224831973..224833573-chr1:225038934..225041311,18	MCF-7	breast:
2	chr1:224702056..224704191-chr1:224831412..224833882,2	MCF-7	breast:
3	chr1:224831768..224834375-chr1:225108469..225110982,2	K562	blood:
4	chr1:224826905..224830184-chr1:224832363..224835221,3	K562	blood:
5	chr1:224827571..224830505-chr1:224833018..224834842,2	K562	blood:

Variant related genes	Relation type
ENSG00000143786	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1036431	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1039265	1.00[CEU][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10495227	0.85[CEU][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10915691	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10915693	1.00[CEU][hapmap];0.80[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10915695	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1106233	0.83[CEU][hapmap]
rs11805320	0.81[CEU][hapmap];0.93[AMR][1000 genomes]
rs12058085	0.85[CEU][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12060334	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12062831	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12068125	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12072810	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12073052	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12077707	1.00[CEU][hapmap];0.80[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12079156	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12088524	1.00[CEU][hapmap];0.83[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12092532	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12096245	0.83[CEU][hapmap]
rs12562581	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12565092	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12567125	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1337538	1.00[CEU][hapmap];0.81[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1369848	0.83[EUR][1000 genomes]
rs1465766	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1465767	0.85[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1499289	0.83[CEU][hapmap];0.91[LWK][hapmap]
rs1499294	0.80[LWK][hapmap]
rs1532557	0.83[CEU][hapmap]
rs16850786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4363402	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs61603030	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61827113	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61827152	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6426147	1.00[CEU][hapmap];0.80[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6695864	0.92[CEU][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7541279	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7554310	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs883116	0.81[CEU][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][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	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12065840	RAB3GAP2	cis	cerebellum	SCAN
rs12065840	PYCR2	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224820400-224840000	Weak transcription	Right Atrium	heart
2	chr1:224826000-224839200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:224826400-224837800	Weak transcription	NHLF	lung
4	chr1:224827000-224839800	Weak transcription	HSMM	muscle
5	chr1:224828600-224834000	Weak transcription	Pancreas	Pancrea
6	chr1:224828600-224837800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:224828800-224853400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:224829800-224835200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:224830800-224835200	Weak transcription	NH-A	brain
10	chr1:224831600-224833800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:224831600-224835600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:224832200-224839800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:224832200-224884400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:224832400-224833600	Enhancers	NHDF-Ad	bronchial
15	chr1:224832800-224834200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:224832800-224837600	Weak transcription	Ovary	ovary
17	chr1:224832800-224838000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:224832800-224869000	Weak transcription	Dnd41	blood
19	chr1:224833200-224833600	Enhancers	HSMMtube	muscle
20	chr1:224833200-224834400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:224833200-224874400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:224833400-224835000	Weak transcription	Fetal Brain Male	brain
23	chr1:224833400-224835200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:224833400-224835200	Weak transcription	Brain Germinal Matrix	brain
25	chr1:224833400-224840600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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