Variant report

Variant	rs1054396
Chromosome Location	chr12:10756855-10756856
allele	A/T
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	POLR2A	chr12:10755951-10758931	K562	blood:	n/a	n/a
2	POLR2A	chr12:10756506-10756995	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:10756231..10758139-chr12:10758556..10760735,3	MCF-7	breast:
2	chr12:10752498..10759716-chr12:10759735..10767266,16	K562	blood:
3	chr12:10750720..10754463-chr12:10754546..10757493,4	K562	blood:
4	chr12:10754715..10757719-chr12:10762132..10766161,5	MCF-7	breast:

Variant related genes	Relation type
KLRAP1	TF binding region
ENSG00000111196	Chromatin interaction
ENSG00000256667	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10083164	0.83[JPT][hapmap]
rs1026442	0.92[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10431297	0.82[JPT][hapmap]
rs1073305	0.82[JPT][hapmap]
rs10743911	1.00[JPT][hapmap]
rs10772334	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10772340	0.82[JPT][hapmap]
rs10772343	0.81[JPT][hapmap]
rs10772347	0.82[JPT][hapmap]
rs10845180	0.92[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10845181	0.84[ASW][hapmap];0.88[CEU][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10845183	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845185	1.00[JPT][hapmap]
rs10845192	0.82[JPT][hapmap]
rs10845194	0.81[JPT][hapmap]
rs10845195	0.82[JPT][hapmap]
rs10845197	0.80[JPT][hapmap]
rs10845198	0.82[JPT][hapmap]
rs11053877	0.92[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11053880	0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11053881	0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs11053882	1.00[JPT][hapmap]
rs12306757	0.87[GIH][hapmap];1.00[JPT][hapmap]
rs12306815	1.00[JPT][hapmap]
rs12811247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1870194	1.00[JPT][hapmap]
rs2125091	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2168749	0.85[CEU][hapmap];0.83[MEX][hapmap];0.86[AMR][1000 genomes]
rs2219382	0.81[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs2290718	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2305853	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2418087	0.82[JPT][hapmap]
rs2418088	0.82[JPT][hapmap]
rs2900513	0.82[JPT][hapmap]
rs3759264	1.00[JPT][hapmap]
rs3759265	0.93[JPT][hapmap]
rs3782674	1.00[JPT][hapmap]
rs4763565	0.96[ASN][1000 genomes]
rs6488316	0.82[JPT][hapmap]
rs7312261	1.00[JPT][hapmap]
rs7313620	0.81[JPT][hapmap]
rs7350557	0.82[JPT][hapmap]
rs7350597	0.82[JPT][hapmap]
rs7968284	0.82[JPT][hapmap]
rs7968819	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7971142	0.82[JPT][hapmap]
rs897880	1.00[JPT][hapmap]
rs897882	1.00[JPT][hapmap]
rs9988929	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv832329	chr12:10677094-10845946	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv973995	chr12:10754447-10758396	Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1054396	C1R	cis	parietal	SCAN
rs1054396	NOP2	cis	cerebellum	SCAN
rs1054396	CLEC4E	cis	parietal	SCAN
rs1054396	SLC2A14	cis	parietal	SCAN
rs1054396	GPRC5A	cis	parietal	SCAN
rs1054396	MAGOHB	cis	cerebellum	SCAN
rs1054396	LOC653113	cis	cerebellum	SCAN
rs1054396	KLRA1	cis	cerebellum	SCAN
rs1054396	TPI1	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10725600-10765000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr12:10725800-10761400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:10726400-10759800	Weak transcription	NHLF	lung
4	chr12:10730000-10762000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:10730600-10764800	Weak transcription	Lung	lung
6	chr12:10730800-10758400	Weak transcription	NHEK	skin
7	chr12:10731600-10760800	Weak transcription	Fetal Brain Female	brain
8	chr12:10732000-10759600	Weak transcription	Fetal Intestine Large	intestine
9	chr12:10732000-10759800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr12:10732200-10759600	Weak transcription	Left Ventricle	heart
11	chr12:10732200-10761400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr12:10732200-10764800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr12:10732400-10759600	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:10732400-10764200	Weak transcription	Pancreas	Pancrea
15	chr12:10732600-10759600	Weak transcription	HMEC	breast
16	chr12:10732800-10759600	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:10733400-10759600	Weak transcription	HUVEC	blood vessel
18	chr12:10733600-10759800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:10733800-10760000	Weak transcription	Fetal Brain Male	brain
20	chr12:10734000-10759400	Weak transcription	Fetal Lung	lung
21	chr12:10734000-10764000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:10734000-10764600	Weak transcription	Thymus	Thymus
23	chr12:10734200-10757400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr12:10734200-10759400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr12:10734200-10759400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr12:10734200-10759400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr12:10734200-10759600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr12:10734200-10762200	Weak transcription	Fetal Muscle Leg	muscle
29	chr12:10734200-10764000	Weak transcription	Fetal Stomach	stomach
30	chr12:10734400-10764600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:10735200-10759600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:10735200-10764600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:10735400-10764000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr12:10736400-10758600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:10738800-10764000	Weak transcription	Fetal Intestine Small	intestine
36	chr12:10739400-10761400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:10742000-10761200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr12:10742600-10757200	Weak transcription	NH-A	brain
39	chr12:10742600-10764600	Weak transcription	Small Intestine	intestine
40	chr12:10742800-10764800	Weak transcription	Psoas Muscle	Psoas
41	chr12:10743400-10759600	Weak transcription	Brain Angular Gyrus	brain
42	chr12:10743400-10759600	Weak transcription	Brain Anterior Caudate	brain
43	chr12:10743400-10765400	Weak transcription	Gastric	stomach
44	chr12:10744000-10765200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr12:10744000-10765400	Weak transcription	Aorta	Aorta
46	chr12:10744200-10757200	Weak transcription	NHDF-Ad	bronchial
47	chr12:10744200-10757600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr12:10744200-10757800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr12:10744200-10759600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr12:10744200-10759600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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