Variant report

Variant	rs55916269
Chromosome Location	chr12:46177534-46177535
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46121334..46123054-chr12:46175648..46177612,2	K562	blood:
2	chr12:46168951..46170529-chr12:46177515..46179157,2	K562	blood:
3	chr12:46171044..46173510-chr12:46175447..46178280,3	K562	blood:

Variant related genes	Relation type
ENSG00000273015	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10161001	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10161062	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10161510	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10880858	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11183135	1.00[EUR][1000 genomes]
rs11183136	1.00[EUR][1000 genomes]
rs11183197	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11183199	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11183202	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12296933	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12297214	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12298597	1.00[EUR][1000 genomes]
rs12301665	1.00[EUR][1000 genomes]
rs12302862	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12305110	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12309988	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12312478	1.00[EUR][1000 genomes]
rs12316361	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12316726	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12321106	1.00[EUR][1000 genomes]
rs28583490	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4522236	1.00[EUR][1000 genomes]
rs56338250	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58253063	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59340060	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6582575	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7132585	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7133123	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7296694	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7303119	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7308856	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7308893	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7309921	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7315365	1.00[EUR][1000 genomes]
rs74081382	1.00[EUR][1000 genomes]
rs74081384	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74081401	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74084208	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7953515	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7964495	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7972650	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7973967	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7975170	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7975408	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7977711	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758306	chr12:46149338-46349891	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759897	chr12:46149338-46349891	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv832396	chr12:46155424-46310583	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv3325128	chr12:46175148-46224560	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46132000-46205200	Weak transcription	HSMM	muscle
2	chr12:46149600-46215400	Weak transcription	Fetal Kidney	kidney
3	chr12:46157400-46199600	Weak transcription	HepG2	liver
4	chr12:46164400-46187800	Weak transcription	Fetal Thymus	thymus
5	chr12:46164400-46193600	Weak transcription	Fetal Stomach	stomach
6	chr12:46164600-46187800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:46164600-46187800	Weak transcription	GM12878-XiMat	blood
8	chr12:46164600-46193400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:46164600-46205200	Weak transcription	Dnd41	blood
10	chr12:46164600-46230000	Weak transcription	Thymus	Thymus
11	chr12:46164800-46193200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:46165200-46187800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr12:46166200-46181200	Weak transcription	Hela-S3	cervix
14	chr12:46166800-46199800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:46167600-46205200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr12:46168600-46193400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:46168800-46181000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:46168800-46193600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:46169000-46178400	Weak transcription	Gastric	stomach
20	chr12:46169000-46181800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr12:46169000-46182600	Weak transcription	NHDF-Ad	bronchial
22	chr12:46169000-46187800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:46169000-46197600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr12:46169000-46202400	Weak transcription	Aorta	Aorta
25	chr12:46169000-46202400	Weak transcription	Left Ventricle	heart
26	chr12:46169000-46202400	Weak transcription	Psoas Muscle	Psoas
27	chr12:46169000-46205200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr12:46169000-46208000	Weak transcription	Brain Angular Gyrus	brain
29	chr12:46169000-46215400	Weak transcription	Fetal Lung	lung
30	chr12:46169200-46182800	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr12:46169200-46190000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:46170000-46184200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:46170200-46182400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:46170200-46183000	Weak transcription	Brain Substantia Nigra	brain
35	chr12:46170200-46193600	Weak transcription	Fetal Intestine Small	intestine
36	chr12:46170400-46182800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr12:46174000-46182800	Weak transcription	A549	lung
38	chr12:46174200-46205000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:46175200-46178600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:46175200-46181000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:46175200-46215400	Weak transcription	Primary B cells from cord blood	blood
42	chr12:46175600-46205200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:46175800-46179000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:46175800-46205200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:46176000-46177600	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr12:46177000-46177600	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr12:46177000-46177800	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr12:46177200-46177600	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr12:46177400-46177600	Enhancers	H1 Cell Line	embryonic stem cell
50	chr12:46177400-46177600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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