Variant report

Variant	rs7302842
Chromosome Location	chr12:105603537-105603538
allele	A/C
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	MXI1	chr12:105603194-105604025	IMR90	lung:	n/a	n/a
2	MAFK	chr12:105603397-105603594	IMR90	lung:	n/a	n/a
3	CEBPB	chr12:105603377-105603563	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105586360..105589934-chr12:105601343..105605180,3	MCF-7	breast:
2	chr12:105602998..105604968-chr12:105605214..105607629,2	MCF-7	breast:

Variant related genes	Relation type
APPL2	TF binding region
ENSG00000136044	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10083185	0.91[ASW][hapmap];0.92[GIH][hapmap];0.90[MKK][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10161513	1.00[ASN][1000 genomes]
rs11112381	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11112389	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11112410	0.88[CEU][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112452	1.00[ASN][1000 genomes]
rs11559871	0.83[EUR][1000 genomes]
rs11829598	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12299366	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299391	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12301914	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304384	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12305766	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307372	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12308444	0.82[EUR][1000 genomes]
rs12311156	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12312965	1.00[CEU][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12317637	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12317804	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321199	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321518	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321534	0.87[CEU][hapmap]
rs12424095	1.00[ASN][1000 genomes]
rs12424191	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424709	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425803	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3910856	0.87[CEU][hapmap]
rs56284118	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56862143	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58780154	1.00[ASN][1000 genomes]
rs59320697	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59593474	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60835294	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60999193	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132816	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133728	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136453	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7138574	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7300130	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305406	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313309	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7315964	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73179990	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73179996	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73179998	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73180001	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73181810	1.00[ASN][1000 genomes]
rs73181818	1.00[ASN][1000 genomes]
rs73181822	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73181825	1.00[ASN][1000 genomes]
rs73181843	1.00[ASN][1000 genomes]
rs73181852	1.00[ASN][1000 genomes]
rs73181856	1.00[ASN][1000 genomes]
rs73181857	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73181869	1.00[ASN][1000 genomes]
rs7964184	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7971630	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975115	1.00[ASN][1000 genomes]
rs7975787	1.00[CEU][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7978034	1.00[CEU][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv455704	chr12:105583877-105651356	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
3	nsv560053	chr12:105583877-105651356	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7302842	KIAA1033	cis	cerebellum	SCAN
rs7302842	ARL1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105546800-105625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:105558800-105615200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:105571400-105617800	Weak transcription	K562	blood
4	chr12:105576400-105606000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:105577000-105607200	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:105577400-105616200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:105577800-105603600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr12:105577800-105605400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr12:105577800-105605600	Strong transcription	Primary B cells from cord blood	blood
10	chr12:105577800-105607400	Strong transcription	Duodenum Mucosa	Duodenum
11	chr12:105578000-105607400	Strong transcription	Fetal Brain Female	brain
12	chr12:105578000-105623200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr12:105578200-105620000	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr12:105579000-105605200	Strong transcription	Fetal Muscle Leg	muscle
15	chr12:105579000-105612400	Strong transcription	Stomach Smooth Muscle	stomach
16	chr12:105580200-105613200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:105581200-105605400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr12:105581800-105605200	Strong transcription	Brain Germinal Matrix	brain
19	chr12:105583600-105605600	Strong transcription	Right Ventricle	heart
20	chr12:105584000-105627000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr12:105587400-105609000	Weak transcription	Fetal Brain Male	brain
22	chr12:105589200-105612200	Weak transcription	Psoas Muscle	Psoas
23	chr12:105589400-105608600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:105589400-105612400	Weak transcription	Fetal Heart	heart
25	chr12:105590200-105620000	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr12:105590400-105618800	Strong transcription	Primary B cells from peripheral blood	blood
27	chr12:105591000-105619400	Strong transcription	Primary T cells from cord blood	blood
28	chr12:105594000-105605400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:105594200-105603600	Strong transcription	Dnd41	blood
30	chr12:105594200-105604400	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr12:105594400-105614400	Weak transcription	Small Intestine	intestine
32	chr12:105594600-105607200	Strong transcription	Fetal Intestine Large	intestine
33	chr12:105594600-105607600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:105595000-105612800	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr12:105595000-105618800	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr12:105595200-105607800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:105595600-105612800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:105595800-105603600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:105595800-105605800	Strong transcription	Adipose Nuclei	Adipose
40	chr12:105595800-105612000	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr12:105595800-105612200	Weak transcription	Right Atrium	heart
42	chr12:105595800-105616600	Strong transcription	Primary hematopoietic stem cells	blood
43	chr12:105596000-105617000	Strong transcription	Fetal Lung	lung
44	chr12:105596200-105605400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr12:105596400-105621800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:105596600-105603800	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr12:105596600-105607600	Strong transcription	Liver	Liver
48	chr12:105597200-105607800	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr12:105599400-105612400	Strong transcription	Brain Anterior Caudate	brain
50	chr12:105599600-105604800	Strong transcription	HSMM	muscle

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