Variant report

Variant	rs5749502
Chromosome Location	chr22:21945096-21945097
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:21944212..21947141-chr22:21982751..21985738,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161179	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1034329	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11089620	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11089629	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11089637	0.84[CEU][hapmap]
rs12158299	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12168958	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12169001	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12484550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs131656	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs131658	0.86[EUR][1000 genomes]
rs131664	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs131665	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs140489	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs140490	0.87[EUR][1000 genomes]
rs140491	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs140492	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs140498	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs140499	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1811069	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs181359	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs181360	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs181361	0.84[EUR][1000 genomes]
rs181363	0.89[EUR][1000 genomes]
rs181366	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2070512	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2256609	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2266959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2266961	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2266963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2266964	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2283789	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2283790	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2298428	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2298429	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2876971	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4820091	0.84[CEU][hapmap]
rs4821104	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4821108	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4821112	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4821114	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4821116	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4821124	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4821130	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5749485	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5749493	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5749495	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5754100	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5754102	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5754166	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5754177	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs5754217	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5754234	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5754238	0.92[EUR][1000 genomes]
rs5754295	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5754323	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5754344	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754352	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5754387	1.00[CEU][hapmap]
rs5754422	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5754426	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5754467	0.92[CEU][hapmap]
rs59391722	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5994638	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5998509	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5998576	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5998599	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5998619	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5998644	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5998672	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66534072	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73166619	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73166622	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73166630	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73166632	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs738127	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs738128	0.85[EUR][1000 genomes]
rs7444	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7445	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8137950	0.86[EUR][1000 genomes]
rs8139079	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8139142	0.86[JPT][hapmap]
rs878825	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9619386	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9621715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1815888	chr22:21486890-21947822	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1065490	chr22:21567219-21949226	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1056096	chr22:21567219-21951562	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv1797475	chr22:21683210-21950089	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv1816994	chr22:21683210-21950089	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	esv1824349	chr22:21683210-21950089	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv1826188	chr22:21683210-21950089	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	esv1851345	chr22:21683210-21950089	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv428386	chr22:21683210-21950089	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv914458	chr22:21747678-22070489	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
11	nsv834145	chr22:21775069-21950089	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
12	nsv482690	chr22:21807513-22016791	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	374 gene(s)	inside rSNPs	diseases
13	nsv1064360	chr22:21809185-21951562	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	esv1823866	chr22:21928916-22131125	Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	374 gene(s)	inside rSNPs	diseases
15	nsv948603	chr22:21928916-22601814	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	422 gene(s)	inside rSNPs	diseases
16	nsv948902	chr22:21928916-22657900	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	426 gene(s)	inside rSNPs	diseases
17	nsv1063962	chr22:21939722-22934593	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	477 gene(s)	inside rSNPs	diseases
18	nsv1058617	chr22:21939922-22934454	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	477 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5749502	CCDC116	cis	Nerve Tibial	GTEx
rs5749502	UBE2L3	Cis_1M	lymphoblastoid	RTeQTL
rs5749502	UBE2L3	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:21924400-21947400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:21925600-21946800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr22:21925800-21946800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr22:21928800-21945600	Weak transcription	Brain Germinal Matrix	brain
5	chr22:21929000-21947000	Weak transcription	HUVEC	blood vessel
6	chr22:21932000-21945200	Weak transcription	A549	lung
7	chr22:21933000-21946800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr22:21933200-21945400	Weak transcription	Colonic Mucosa	Colon
9	chr22:21933400-21948000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr22:21933800-21946200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr22:21934600-21945200	Weak transcription	Fetal Intestine Large	intestine
12	chr22:21934600-21945400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr22:21936000-21948400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr22:21937400-21945200	Weak transcription	Aorta	Aorta
15	chr22:21937400-21946000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr22:21937600-21947400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr22:21937800-21965400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr22:21938000-21947200	Weak transcription	Fetal Kidney	kidney
19	chr22:21939000-21954000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr22:21939600-21983200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr22:21940200-21945400	Weak transcription	Primary T cells from cord blood	blood
22	chr22:21941200-21945200	Enhancers	Primary B cells from peripheral blood	blood
23	chr22:21941200-21946000	Enhancers	Primary B cells from cord blood	blood
24	chr22:21941800-21946600	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr22:21942200-21945200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr22:21942200-21945400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr22:21942200-21947200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr22:21942400-21945200	Weak transcription	Lung	lung
29	chr22:21942400-21947800	Weak transcription	Fetal Brain Male	brain
30	chr22:21942600-21945200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr22:21942600-21945200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr22:21942600-21945200	Weak transcription	Stomach Mucosa	stomach
33	chr22:21942600-21945400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr22:21942600-21945600	Weak transcription	Fetal Brain Female	brain
35	chr22:21942600-21946800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr22:21942600-21947000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr22:21942600-21960800	Weak transcription	Small Intestine	intestine
38	chr22:21942800-21945200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr22:21942800-21945200	Weak transcription	Brain Angular Gyrus	brain
40	chr22:21942800-21945200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr22:21942800-21945400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr22:21942800-21945400	Weak transcription	NHLF	lung
43	chr22:21942800-21945800	Weak transcription	HSMMtube	muscle
44	chr22:21942800-21946800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr22:21942800-21947400	Weak transcription	NH-A	brain
46	chr22:21943000-21946800	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr22:21943400-21945600	Genic enhancers	K562	blood
48	chr22:21943400-21963600	Strong transcription	Fetal Intestine Small	intestine
49	chr22:21943600-21946400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr22:21943600-21947400	Enhancers	Left Ventricle	heart

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