Variant report

Variant	rs2279862
Chromosome Location	chr11:66135179-66135180
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:66096831..66099072-chr11:66133272..66136044,2	MCF-7	breast:
2	chr11:66100823..66106592-chr11:66129818..66135879,7	MCF-7	breast:
3	chr11:66135052..66136589-chr19:10612496..10614660,2	MCF-7	breast:
4	chr11:66133310..66136100-chr20:46287842..46289373,2	MCF-7	breast:
5	chr11:66102881..66107086-chr11:66131978..66137465,5	MCF-7	breast:
6	chr11:66108426..66118730-chr11:66133678..66141000,25	MCF-7	breast:
7	chr11:66036063..66037921-chr11:66134364..66136433,2	K562	blood:
8	chr11:66103854..66118324-chr11:66119048..66141728,55	K562	blood:

No data

Variant related genes	Relation type
ENSG00000174744	Chromatin interaction
ENSG00000174791	Chromatin interaction
ENSG00000174684	Chromatin interaction
ENSG00000254756	Chromatin interaction
ENSG00000255468	Chromatin interaction
ENSG00000079999	Chromatin interaction
ENSG00000196562	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1039594	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1047029	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10750784	1.00[CEU][hapmap];0.83[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10791869	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10791872	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10791874	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10791876	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10896111	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10896112	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896115	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10896116	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11227465	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11601396	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11823140	0.96[CEU][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs12416747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12576293	0.84[ASN][1000 genomes]
rs12576299	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12577196	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12577917	0.81[JPT][hapmap]
rs12785321	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12785651	0.83[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12786563	0.83[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12794121	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1546358	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1784029	0.92[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1785633	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1785639	0.84[ASW][hapmap];0.96[CEU][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.88[EUR][1000 genomes]
rs1892938	0.91[ASW][hapmap];0.83[LWK][hapmap];0.84[YRI][hapmap]
rs1892940	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2236679	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2279861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282530	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2282531	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs3016767	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3177514	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34043951	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4244813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4466842	0.88[CEU][hapmap]
rs4930177	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4930178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4930179	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4930181	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4930360	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4930362	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4930363	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4930366	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4930368	0.83[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55998145	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56123976	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56321771	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61891449	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6591213	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6591215	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6591217	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66810040	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67780191	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7104253	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7104570	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7105015	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7105401	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7107191	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7110944	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7117630	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7126018	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73489638	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7938676	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7939111	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7940980	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs905770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs947978	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
4	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
5	nsv897772	chr11:66018155-66254085	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
6	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv832193	chr11:66120339-66278805	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2279862	SNX32	cis	parietal	SCAN
rs2279862	ALDH3B1	cis	parietal	SCAN
rs2279862	OVOL1	cis	parietal	SCAN
rs2279862	ASRGL1	cis	parietal	SCAN
rs2279862	RIN1	cis	Whole Blood	GTEx
rs2279862	ESRRA	cis	cerebellum	SCAN
rs2279862	SCYL1	cis	lymphoblastoid	seeQTL
rs2279862	CCDC87	cis	parietal	SCAN
rs2279862	SLC25A45	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66116000-66135800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr11:66116000-66137200	Weak transcription	Fetal Kidney	kidney
3	chr11:66116000-66138400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr11:66116000-66138400	Weak transcription	Brain Hippocampus Middle	brain
5	chr11:66116000-66138400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr11:66116000-66138400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:66116200-66137000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr11:66116200-66137400	Weak transcription	Brain Angular Gyrus	brain
9	chr11:66116200-66137400	Weak transcription	Brain Anterior Caudate	brain
10	chr11:66116200-66137800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr11:66116200-66138400	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr11:66116800-66137200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr11:66116800-66137400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr11:66116800-66138400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr11:66117000-66138200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr11:66119000-66137800	Weak transcription	A549	lung
17	chr11:66121400-66138400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr11:66121800-66138400	Weak transcription	Primary B cells from cord blood	blood
19	chr11:66122000-66137400	Strong transcription	Fetal Intestine Small	intestine
20	chr11:66126200-66136400	Strong transcription	Fetal Stomach	stomach
21	chr11:66127400-66137200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr11:66127400-66137400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr11:66127600-66137600	Weak transcription	NHEK	skin
24	chr11:66127800-66136000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:66128000-66137000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr11:66128200-66137000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr11:66128200-66137200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:66128200-66138600	Weak transcription	Dnd41	blood
29	chr11:66128600-66135800	Weak transcription	Psoas Muscle	Psoas
30	chr11:66129000-66136000	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr11:66129200-66137000	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr11:66129200-66137000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr11:66129600-66137000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr11:66129800-66137000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr11:66129800-66137200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr11:66130200-66136600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:66130600-66136200	Weak transcription	Fetal Thymus	thymus
38	chr11:66131000-66137400	Weak transcription	Colonic Mucosa	Colon
39	chr11:66131000-66138600	Weak transcription	Liver	Liver
40	chr11:66131400-66136000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr11:66131400-66138400	Weak transcription	Thymus	Thymus
42	chr11:66131600-66137000	Weak transcription	Stomach Mucosa	stomach
43	chr11:66131800-66137400	Weak transcription	Brain Germinal Matrix	brain
44	chr11:66132000-66137200	Weak transcription	Adipose Nuclei	Adipose
45	chr11:66132200-66136000	Weak transcription	Fetal Heart	heart
46	chr11:66132600-66135800	Strong transcription	Fetal Muscle Leg	muscle
47	chr11:66132600-66137000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr11:66132600-66137000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr11:66132800-66136400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr11:66132800-66136400	Strong transcription	Duodenum Mucosa	Duodenum

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