Variant report

Variant	rs947978
Chromosome Location	chr11:66108660-66108661
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66108426..66118730-chr11:66133678..66141000,25	MCF-7	breast:
2	chr11:66092468..66094191-chr11:66107437..66109172,2	K562	blood:
3	chr11:66103854..66118324-chr11:66119048..66141728,55	K562	blood:

Variant related genes	Relation type
ENSG00000174669	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1039594	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1047029	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10750784	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10791869	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10791872	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10791874	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10791876	0.84[EUR][1000 genomes]
rs10896111	1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10896112	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10896115	0.85[EUR][1000 genomes]
rs10896116	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11227465	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11601396	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11823140	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12416747	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12576299	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12577196	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12785321	0.83[EUR][1000 genomes]
rs12785651	0.83[ASW][hapmap];0.96[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap];0.83[EUR][1000 genomes]
rs12786563	0.83[ASW][hapmap];0.96[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap];0.83[EUR][1000 genomes]
rs12794121	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1546358	0.85[EUR][1000 genomes]
rs1784029	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1785633	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[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];1.00[TSI][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1785639	0.84[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1892938	0.91[ASW][hapmap];0.94[LWK][hapmap];0.82[MKK][hapmap];0.84[YRI][hapmap]
rs1892940	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236679	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279861	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];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2279862	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]
rs2282530	0.96[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs2282531	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3016767	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3177514	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34043951	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4244813	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4466842	0.88[CEU][hapmap]
rs4930177	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4930178	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4930179	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4930181	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4930360	0.81[EUR][1000 genomes]
rs4930362	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4930363	0.85[EUR][1000 genomes]
rs4930366	0.82[EUR][1000 genomes]
rs4930368	0.83[ASW][hapmap];0.96[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap];0.83[EUR][1000 genomes]
rs55998145	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56123976	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56321771	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61891449	0.86[EUR][1000 genomes]
rs6591213	1.00[CEU][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6591215	0.85[EUR][1000 genomes]
rs6591217	0.84[EUR][1000 genomes]
rs66810040	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7104253	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7104570	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7105015	0.83[EUR][1000 genomes]
rs7105401	0.84[EUR][1000 genomes]
rs7107191	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7110944	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7117630	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7126018	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73489638	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7938676	0.82[EUR][1000 genomes]
rs7939111	0.84[EUR][1000 genomes]
rs7940980	0.82[EUR][1000 genomes]
rs905770	1.00[CEU][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv897781	chr11:66095967-66116911	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	nsv897782	chr11:66099222-66116911	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
9	esv3328878	chr11:66107076-66111474	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
10	nsv897783	chr11:66107527-66118676	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs947978	ESRRA	cis	cerebellum	SCAN
rs947978	ALDH3B1	cis	parietal	SCAN
rs947978	SCYL1	cis	lymphoblastoid	seeQTL
rs947978	OVOL1	cis	parietal	SCAN
rs947978	SLC25A45	cis	parietal	SCAN
rs947978	RIN1	cis	Whole Blood	GTEx
rs947978	CCDC87	cis	parietal	SCAN
rs947978	SNX32	cis	parietal	SCAN
rs947978	ASRGL1	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66098400-66108800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:66104200-66109000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:66104400-66110400	Strong transcription	Dnd41	blood
4	chr11:66104600-66109000	Weak transcription	Fetal Kidney	kidney
5	chr11:66104600-66109800	Strong transcription	Colonic Mucosa	Colon
6	chr11:66104600-66109800	Strong transcription	Lung	lung
7	chr11:66104600-66110000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:66104600-66110400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr11:66104600-66110400	Strong transcription	Fetal Intestine Large	intestine
10	chr11:66104600-66110400	Strong transcription	Right Ventricle	heart
11	chr11:66104600-66110800	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr11:66104600-66111600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:66104800-66108800	Strong transcription	Gastric	stomach
14	chr11:66104800-66109600	Strong transcription	Brain Substantia Nigra	brain
15	chr11:66104800-66109600	Strong transcription	Rectal Smooth Muscle	rectum
16	chr11:66104800-66109800	Strong transcription	Left Ventricle	heart
17	chr11:66104800-66110000	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr11:66104800-66110000	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr11:66104800-66110000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr11:66104800-66110400	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr11:66104800-66110800	Strong transcription	Adipose Nuclei	Adipose
22	chr11:66104800-66110800	Strong transcription	Brain Cingulate Gyrus	brain
23	chr11:66104800-66110800	Weak transcription	Psoas Muscle	Psoas
24	chr11:66104800-66111000	Strong transcription	Primary T cells from cord blood	blood
25	chr11:66104800-66111200	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr11:66104800-66111200	Strong transcription	Placenta	Placenta
27	chr11:66105000-66109000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr11:66105000-66109600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr11:66105000-66109800	Strong transcription	Liver	Liver
30	chr11:66105000-66110000	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr11:66105000-66110000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr11:66105000-66110400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr11:66105000-66110600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr11:66105000-66111000	Strong transcription	Duodenum Mucosa	Duodenum
35	chr11:66105000-66111000	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr11:66105000-66111200	Strong transcription	Fetal Intestine Small	intestine
37	chr11:66105200-66109800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
38	chr11:66105200-66110000	Strong transcription	Brain Hippocampus Middle	brain
39	chr11:66105200-66110400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr11:66105200-66110400	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr11:66105200-66110600	Strong transcription	Primary B cells from peripheral blood	blood
42	chr11:66105200-66110800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr11:66105200-66110800	Strong transcription	Brain Germinal Matrix	brain
44	chr11:66105200-66110800	Strong transcription	Fetal Stomach	stomach
45	chr11:66105200-66111000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr11:66105200-66111000	Strong transcription	Fetal Thymus	thymus
47	chr11:66105200-66111000	Strong transcription	Thymus	Thymus
48	chr11:66105200-66111200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr11:66105400-66108800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr11:66105400-66109600	Strong transcription	Primary hematopoietic stem cells	blood

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