Variant report

Variant	rs12911094
Chromosome Location	chr15:56408451-56408452
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56407805..56409350-chr15:56422499..56425257,2	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11629483	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11631191	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12905899	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12907263	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12911427	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12914260	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12914640	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1372753	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1442640	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1829542	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2119937	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2249090	0.85[CEU][hapmap]
rs2414464	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2460647	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2460648	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2460650	0.92[CEU][hapmap]
rs2682044	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2682051	0.92[CEU][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs2682054	0.92[CEU][hapmap]
rs2682059	0.92[CEU][hapmap]
rs2713923	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2713924	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2713926	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2713933	0.92[CEU][hapmap]
rs2713936	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs2713938	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2713941	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2718915	0.82[AMR][1000 genomes]
rs2718934	0.92[CEU][hapmap]
rs2718941	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2725854	0.96[CEU][hapmap];0.84[MKK][hapmap];0.88[YRI][hapmap]
rs2725870	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2947021	0.85[CEU][hapmap]
rs34044869	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34144128	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34224072	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34386737	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34756325	0.86[ASN][1000 genomes]
rs35082998	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35722267	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35749329	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35972806	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4310791	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4310792	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4774231	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4774232	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4774847	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59432349	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62044082	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62044110	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62044111	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6493835	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7165270	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7168319	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7174823	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7175745	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7176107	0.88[CEU][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs7496025	0.82[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8024031	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8028353	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8029114	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8032242	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8033653	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9672886	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9672928	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[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	esv2761872	chr15:56211065-56426501	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv833018	chr15:56325799-56492535	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1045906	chr15:56333180-56473614	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12911094	RFX7	cis	Skin Sun Exposed Lower leg	GTEx
rs12911094	RFX7	cis	lung	GTEx
rs12911094	RFX7	cis	Adipose Subcutaneous	GTEx
rs12911094	RFX7	cis	lymphoblastoid	seeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56388800-56411600	Weak transcription	Fetal Stomach	stomach
2	chr15:56388800-56414400	Weak transcription	Thymus	Thymus
3	chr15:56388800-56418400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr15:56388800-56433000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr15:56388800-56437200	Weak transcription	Pancreas	Pancrea
6	chr15:56388800-56441600	Weak transcription	Lung	lung
7	chr15:56389400-56418400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr15:56389400-56418400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr15:56389600-56414400	Weak transcription	HSMMtube	muscle
10	chr15:56389800-56415600	Weak transcription	Placenta	Placenta
11	chr15:56390400-56414400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr15:56390600-56412600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:56390600-56413200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr15:56390600-56414200	Weak transcription	Fetal Lung	lung
15	chr15:56390600-56414200	Weak transcription	Left Ventricle	heart
16	chr15:56390600-56414600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:56390600-56416400	Weak transcription	HUVEC	blood vessel
18	chr15:56390600-56417400	Weak transcription	Adipose Nuclei	Adipose
19	chr15:56390600-56418000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:56390800-56418600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr15:56391000-56411800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr15:56391800-56415800	Weak transcription	Ovary	ovary
23	chr15:56392600-56417200	Weak transcription	Brain Hippocampus Middle	brain
24	chr15:56393800-56412400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:56394000-56414200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:56394000-56418200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr15:56394200-56417000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr15:56394400-56411000	Weak transcription	Liver	Liver
29	chr15:56394400-56411600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr15:56394400-56414000	Weak transcription	HMEC	breast
31	chr15:56394400-56414200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr15:56394400-56414200	Weak transcription	NH-A	brain
33	chr15:56394800-56414800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr15:56395000-56411600	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr15:56395000-56412600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr15:56395000-56415800	Weak transcription	Fetal Thymus	thymus
37	chr15:56395000-56418200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr15:56395200-56414200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:56395600-56411400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr15:56396000-56412600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr15:56397000-56408600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr15:56397000-56410600	Weak transcription	Psoas Muscle	Psoas
43	chr15:56397000-56414200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr15:56397200-56414200	Weak transcription	Primary T cells from cord blood	blood
45	chr15:56397400-56412400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr15:56397400-56412600	Weak transcription	Primary B cells from peripheral blood	blood
47	chr15:56398400-56413200	Weak transcription	Dnd41	blood
48	chr15:56399200-56412800	Weak transcription	HepG2	liver
49	chr15:56402400-56408600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr15:56405200-56410800	Weak transcription	Primary hematopoietic stem cells	blood

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