Variant report

Variant	rs3816567
Chromosome Location	chr12:10745033-10745034
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:10744830..10746958-chr12:10764492..10766186,2	K562	blood:
2	chr12:10738663..10741560-chr12:10743717..10745225,2	MCF-7	breast:
3	chr12:10743385..10746001-chr12:10752818..10754982,2	K562	blood:

Variant related genes	Relation type
ENSG00000111196	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10734838	0.80[ASN][1000 genomes]
rs10743910	0.80[ASN][1000 genomes]
rs10772312	0.82[ASN][1000 genomes]
rs10772315	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10772316	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10772317	0.81[ASN][1000 genomes]
rs10772319	0.80[ASN][1000 genomes]
rs10772321	0.80[ASN][1000 genomes]
rs10772323	0.80[ASN][1000 genomes]
rs10772324	0.81[ASN][1000 genomes]
rs10772326	0.80[ASN][1000 genomes]
rs10772327	0.80[ASN][1000 genomes]
rs10772329	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10845161	0.94[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10845165	0.82[ASN][1000 genomes]
rs10845166	0.81[ASN][1000 genomes]
rs10845172	0.80[ASN][1000 genomes]
rs10845174	0.82[ASN][1000 genomes]
rs10845175	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11053857	0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11053859	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11053865	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11053869	0.80[ASN][1000 genomes]
rs11053870	0.80[ASN][1000 genomes]
rs11053871	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11611202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12423957	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1915323	0.80[ASN][1000 genomes]
rs2002156	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2002157	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2125092	0.81[ASN][1000 genomes]
rs2125095	0.81[ASN][1000 genomes]
rs2168750	0.80[ASN][1000 genomes]
rs2417745	0.81[JPT][hapmap]
rs2417746	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2607883	0.80[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2607888	0.85[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2607891	0.81[JPT][hapmap]
rs2607892	0.81[JPT][hapmap]
rs2607895	0.81[JPT][hapmap]
rs2607898	0.80[JPT][hapmap]
rs2682476	0.81[JPT][hapmap]
rs28403396	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28701155	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3867478	0.81[ASN][1000 genomes]
rs3983544	0.80[ASN][1000 genomes]
rs3983545	0.80[ASN][1000 genomes]
rs3983546	0.80[ASN][1000 genomes]
rs4237928	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4476009	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4763528	0.81[ASN][1000 genomes]
rs4763531	0.81[ASN][1000 genomes]
rs4763532	0.81[ASN][1000 genomes]
rs4763547	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4763548	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4763555	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4763559	0.80[ASN][1000 genomes]
rs55837119	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58917785	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60367665	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61913124	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6488306	0.85[CHD][hapmap];0.95[JPT][hapmap]
rs6488307	0.80[ASN][1000 genomes]
rs7134658	0.80[ASN][1000 genomes]
rs7134908	0.80[ASN][1000 genomes]
rs7136964	0.82[ASN][1000 genomes]
rs7137465	0.82[ASN][1000 genomes]
rs7306285	0.80[ASN][1000 genomes]
rs7306724	0.82[ASN][1000 genomes]
rs7978850	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7980411	0.80[ASN][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	nsv1039120	chr12:10675930-10755446	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	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
3	esv999821	chr12:10742119-10749949	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3816567	KLRC3	cis	parietal	SCAN
rs3816567	KLRC2	cis	cerebellum	SCAN
rs3816567	MAGOHB	cis	parietal	SCAN

Chromatin state (count:104 , 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	chr12:10725800-10753400	Weak transcription	Osteobl	bone
3	chr12:10725800-10761400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:10726400-10759800	Weak transcription	NHLF	lung
5	chr12:10726800-10756600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:10730000-10762000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:10730600-10764800	Weak transcription	Lung	lung
8	chr12:10730800-10746200	Weak transcription	Fetal Thymus	thymus
9	chr12:10730800-10758400	Weak transcription	NHEK	skin
10	chr12:10731200-10756400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr12:10731400-10753200	Weak transcription	Primary B cells from cord blood	blood
12	chr12:10731600-10760800	Weak transcription	Fetal Brain Female	brain
13	chr12:10732000-10759600	Weak transcription	Fetal Intestine Large	intestine
14	chr12:10732000-10759800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr12:10732200-10745800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:10732200-10759600	Weak transcription	Left Ventricle	heart
17	chr12:10732200-10761400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:10732200-10764800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:10732400-10759600	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:10732400-10764200	Weak transcription	Pancreas	Pancrea
21	chr12:10732600-10759600	Weak transcription	HMEC	breast
22	chr12:10732800-10759600	Weak transcription	Brain Hippocampus Middle	brain
23	chr12:10733400-10746000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr12:10733400-10748000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr12:10733400-10759600	Weak transcription	HUVEC	blood vessel
26	chr12:10733600-10759800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:10733800-10753400	Weak transcription	Dnd41	blood
28	chr12:10733800-10760000	Weak transcription	Fetal Brain Male	brain
29	chr12:10734000-10747600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr12:10734000-10753200	Weak transcription	Liver	Liver
31	chr12:10734000-10759400	Weak transcription	Fetal Lung	lung
32	chr12:10734000-10764000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:10734000-10764600	Weak transcription	Thymus	Thymus
34	chr12:10734200-10749200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr12:10734200-10755200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:10734200-10757400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr12:10734200-10759400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr12:10734200-10759400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr12:10734200-10759400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr12:10734200-10759600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr12:10734200-10762200	Weak transcription	Fetal Muscle Leg	muscle
42	chr12:10734200-10764000	Weak transcription	Fetal Stomach	stomach
43	chr12:10734400-10753600	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr12:10734400-10754400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr12:10734400-10754600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr12:10734400-10756600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr12:10734400-10764600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:10734600-10748800	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr12:10735200-10753200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:10735200-10759600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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