Variant report

Variant	rs11048195
Chromosome Location	chr12:9105923-9105924
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	KAP1	chr12:9105602-9105937	K562	blood:	n/a	n/a
2	SETDB1	chr12:9105632-9105975	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:9103173..9107180-chr12:9112850..9116183,4	K562	blood:
2	chr12:9102147..9104333-chr12:9105347..9108888,4	MCF-7	breast:
3	chr12:9103173..9105935-chr12:9114683..9116241,2	K562	blood:

Variant related genes	Relation type
M6PR	TF binding region
ENSG00000139187	Chromatin interaction
ENSG00000003056	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10129061	0.96[CHB][hapmap];0.83[ASN][1000 genomes]
rs10400516	0.81[ASN][1000 genomes]
rs1049925	0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1073159	0.82[EUR][1000 genomes]
rs10743568	0.82[ASN][1000 genomes]
rs10771238	0.82[ASN][1000 genomes]
rs10842537	0.84[EUR][1000 genomes]
rs10842660	0.93[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10842662	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11047953	0.84[EUR][1000 genomes]
rs11048023	0.88[EUR][1000 genomes]
rs11048190	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11048264	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11048337	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11048338	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11048344	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11048345	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11048434	0.91[JPT][hapmap]
rs1124402	0.83[EUR][1000 genomes]
rs11494569	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11494570	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11611106	0.96[CEU][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs11613650	0.83[EUR][1000 genomes]
rs11614202	0.89[ASN][1000 genomes]
rs12371786	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12422905	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12423746	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12423817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12424026	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12581860	0.83[AMR][1000 genomes]
rs12812913	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12814670	0.83[EUR][1000 genomes]
rs12815310	0.83[EUR][1000 genomes]
rs12820395	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12821842	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12823100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12824140	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12824212	0.91[JPT][hapmap]
rs12824380	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12827055	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12827988	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12828902	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12833375	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1476911	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805248	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1805677	0.91[JPT][hapmap]
rs1805719	0.91[JPT][hapmap]
rs1805721	0.93[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1805722	0.93[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1805723	0.93[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1805724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805725	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1805727	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1805732	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1805733	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805735	0.92[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs1805736	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1805737	0.91[EUR][1000 genomes]
rs1805745	0.84[EUR][1000 genomes]
rs1805754	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs1805761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1805765	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1805784	0.84[EUR][1000 genomes]
rs2041624	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2041625	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2080116	0.93[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2080117	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2110190	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2110191	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2110192	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2110193	0.83[EUR][1000 genomes]
rs2159961	0.96[CEU][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes]
rs2377671	0.84[ASN][1000 genomes]
rs2377672	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2377673	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2377674	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34285491	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34798934	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35870866	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4254119	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4309200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4639983	0.96[CHB][hapmap];0.83[ASN][1000 genomes]
rs4883203	0.82[ASN][1000 genomes]
rs6832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7300767	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7301381	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7302417	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7303776	0.83[EUR][1000 genomes]
rs7309922	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7314942	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7315055	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7957321	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7961355	0.83[ASN][1000 genomes]
rs933462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs987917	0.96[CHB][hapmap];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832327	chr12:9081779-9246220	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11048195	KLRG1	cis	multi-tissue	Pritchard
rs11048195	KLRG1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9103000-9109400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:9103400-9112000	Weak transcription	Pancreas	Pancrea
3	chr12:9103400-9116400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:9103600-9110400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:9103600-9114000	Weak transcription	Fetal Kidney	kidney
6	chr12:9103600-9114200	Weak transcription	Aorta	Aorta
7	chr12:9103600-9114400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:9103600-9114600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr12:9103800-9107200	Flanking Active TSS	Primary T cells from cord blood	blood
10	chr12:9104000-9106000	Weak transcription	Fetal Brain Female	brain
11	chr12:9104000-9108400	Weak transcription	Fetal Muscle Leg	muscle
12	chr12:9104000-9108400	Weak transcription	Right Ventricle	heart
13	chr12:9104000-9108600	Weak transcription	Fetal Stomach	stomach
14	chr12:9104000-9108600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr12:9104000-9108800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:9104000-9110400	Weak transcription	A549	lung
17	chr12:9104000-9111000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr12:9104000-9113200	Weak transcription	HepG2	liver
19	chr12:9104000-9114400	Weak transcription	Psoas Muscle	Psoas
20	chr12:9104200-9106000	Weak transcription	Primary B cells from cord blood	blood
21	chr12:9104400-9111200	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr12:9104600-9106400	Enhancers	Primary T cells fromperipheralblood	blood
23	chr12:9104600-9107200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr12:9104600-9110400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr12:9104600-9113800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr12:9104800-9106000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr12:9104800-9106400	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr12:9104800-9109600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
29	chr12:9105000-9106600	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr12:9105000-9106600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr12:9105000-9108400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:9105000-9108800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr12:9105000-9113600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr12:9105000-9113800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:9105200-9106800	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:9105200-9107400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
37	chr12:9105200-9107400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
38	chr12:9105200-9107400	ZNF genes & repeats	Dnd41	blood
39	chr12:9105400-9106000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:9105400-9106000	ZNF genes & repeats	Fetal Thymus	thymus
41	chr12:9105400-9106200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
42	chr12:9105400-9106200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr12:9105400-9107000	ZNF genes & repeats	Liver	Liver
44	chr12:9105400-9107200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr12:9105400-9107400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
46	chr12:9105600-9106000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr12:9105600-9106200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr12:9105600-9106200	ZNF genes & repeats	Fetal Intestine Small	intestine
49	chr12:9105600-9106600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
50	chr12:9105600-9106600	Strong transcription	Left Ventricle	heart

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