Variant report

Variant	rs643772
Chromosome Location	chr18:39581432-39581433
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:39533961..39535776-chr18:39581404..39583665,2	K562	blood:
2	chr18:39580973..39583765-chr18:39598870..39601571,2	K562	blood:
3	chr18:39581260..39583124-chr18:39585047..39587391,2	MCF-7	breast:
4	chr18:39549732..39552143-chr18:39580474..39582675,2	K562	blood:

Variant related genes	Relation type
ENSG00000078142	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10502776	1.00[CEU][hapmap]
rs1142044	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11873469	1.00[EUR][1000 genomes]
rs11873602	1.00[EUR][1000 genomes]
rs11874766	1.00[EUR][1000 genomes]
rs11874775	1.00[EUR][1000 genomes]
rs11874814	1.00[EUR][1000 genomes]
rs11874830	1.00[EUR][1000 genomes]
rs11876547	1.00[EUR][1000 genomes]
rs11876578	1.00[EUR][1000 genomes]
rs11877901	1.00[EUR][1000 genomes]
rs1540057	1.00[EUR][1000 genomes]
rs16975441	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16975447	1.00[EUR][1000 genomes]
rs16975463	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975466	1.00[EUR][1000 genomes]
rs16975521	1.00[EUR][1000 genomes]
rs2469471	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs490578	1.00[EUR][1000 genomes]
rs493100	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs525369	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs542870	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55655849	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs563840	1.00[EUR][1000 genomes]
rs56411890	1.00[EUR][1000 genomes]
rs56751463	1.00[EUR][1000 genomes]
rs56979511	1.00[EUR][1000 genomes]
rs57208863	1.00[EUR][1000 genomes]
rs575366	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58298297	1.00[EUR][1000 genomes]
rs583163	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58390786	1.00[EUR][1000 genomes]
rs584022	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs586797	1.00[EUR][1000 genomes]
rs58881642	1.00[EUR][1000 genomes]
rs591870	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs593689	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59910026	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs606366	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs608428	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs616575	1.00[EUR][1000 genomes]
rs633541	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs635560	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs640064	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs640460	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs645148	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs647084	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6507453	1.00[EUR][1000 genomes]
rs6507454	1.00[EUR][1000 genomes]
rs655693	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs659950	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6650669	1.00[EUR][1000 genomes]
rs667346	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs669235	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs670429	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs674380	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs684091	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7229485	1.00[EUR][1000 genomes]
rs7237185	1.00[EUR][1000 genomes]
rs7237815	1.00[EUR][1000 genomes]
rs7238919	1.00[EUR][1000 genomes]
rs7239880	1.00[EUR][1000 genomes]
rs7240066	1.00[EUR][1000 genomes]
rs7241399	1.00[EUR][1000 genomes]
rs7242077	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7245131	1.00[EUR][1000 genomes]
rs7343027	1.00[EUR][1000 genomes]
rs73448558	1.00[EUR][1000 genomes]
rs73451096	1.00[EUR][1000 genomes]
rs73452235	1.00[EUR][1000 genomes]
rs73452297	1.00[EUR][1000 genomes]
rs73452300	1.00[EUR][1000 genomes]
rs73453013	1.00[EUR][1000 genomes]
rs73454552	1.00[EUR][1000 genomes]
rs73454573	1.00[EUR][1000 genomes]
rs73454580	1.00[EUR][1000 genomes]
rs73454581	1.00[EUR][1000 genomes]
rs73454593	1.00[EUR][1000 genomes]
rs73454596	1.00[EUR][1000 genomes]
rs73454602	1.00[EUR][1000 genomes]
rs73950814	1.00[EUR][1000 genomes]
rs8084037	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs8085708	1.00[EUR][1000 genomes]
rs8089142	1.00[EUR][1000 genomes]
rs8090403	1.00[EUR][1000 genomes]
rs8095945	1.00[EUR][1000 genomes]
rs9948650	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9965647	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv1066869	chr18:38742896-39680723	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS 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	7 gene(s)	inside rSNPs	diseases
2	nsv543685	chr18:38742896-39680723	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv949609	chr18:39126941-40070286	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv431979	chr18:39255558-39696452	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised 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
5	nsv1066029	chr18:39322920-39623625	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv543686	chr18:39322920-39623625	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv909566	chr18:39327962-39688452	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	esv34153	chr18:39398768-39872265	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv909567	chr18:39470190-39652939	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
10	nsv909568	chr18:39491873-39768746	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39536000-39621800	Weak transcription	Stomach Mucosa	stomach
2	chr18:39536800-39633600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr18:39545600-39583600	Weak transcription	Small Intestine	intestine
4	chr18:39548400-39670000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr18:39549200-39582800	Weak transcription	Psoas Muscle	Psoas
6	chr18:39558200-39594800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr18:39558200-39603800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr18:39562800-39585600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr18:39563800-39582800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr18:39563800-39583400	Weak transcription	Right Ventricle	heart
11	chr18:39563800-39585200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr18:39564200-39586400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr18:39564600-39586600	Strong transcription	Primary B cells from cord blood	blood
14	chr18:39564600-39606400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr18:39565000-39597200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr18:39565200-39583600	Weak transcription	Esophagus	oesophagus
17	chr18:39567000-39587200	Strong transcription	Liver	Liver
18	chr18:39568000-39588400	Strong transcription	Primary B cells from peripheral blood	blood
19	chr18:39568000-39588600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr18:39568000-39588800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr18:39569200-39586400	Strong transcription	Dnd41	blood
22	chr18:39569800-39582400	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr18:39570800-39587200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr18:39572000-39654400	Weak transcription	Colonic Mucosa	Colon
25	chr18:39573200-39585800	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr18:39573200-39588000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr18:39573200-39588200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr18:39573200-39592000	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr18:39573400-39586400	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr18:39573400-39586600	Strong transcription	Adipose Nuclei	Adipose
31	chr18:39573400-39587200	Strong transcription	Fetal Intestine Large	intestine
32	chr18:39573400-39592200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr18:39573600-39582000	Strong transcription	Duodenum Mucosa	Duodenum
34	chr18:39573600-39587400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr18:39573800-39588600	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr18:39574800-39589600	Strong transcription	GM12878-XiMat	blood
37	chr18:39574800-39603600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr18:39575200-39586400	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr18:39575400-39586600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr18:39575600-39586800	Strong transcription	Primary T cells from cord blood	blood
41	chr18:39577000-39582400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr18:39577200-39603400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr18:39577400-39581600	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr18:39577400-39582600	Weak transcription	Colon Smooth Muscle	Colon
45	chr18:39577400-39582800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr18:39577400-39583200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr18:39577400-39588400	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr18:39577400-39610000	Weak transcription	Fetal Brain Male	brain
49	chr18:39578000-39583400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr18:39578000-39587000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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