Variant report

Variant	rs12461622
Chromosome Location	chr19:35704062-35704063
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:35703283..35706238-chr19:35738621..35741297,3	MCF-7	breast:
2	chr19:35703379..35705750-chr19:35757891..35759671,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LSR-1	chr19:35704060-35704688	XLOC_013049

Variant related genes	Relation type
ENSG00000105699	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11084807	0.87[EUR][1000 genomes]
rs12978960	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1614514	0.82[EUR][1000 genomes]
rs1633923	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1688009	0.83[ASN][1000 genomes]
rs2018697	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4805115	0.94[EUR][1000 genomes]
rs4806113	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs517986	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs565918	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6510471	0.95[EUR][1000 genomes]
rs7250545	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv1067541	chr19:35698638-35712439	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1066553	chr19:35698638-35749563	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	esv2763203	chr19:35700047-35738400	Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35693400-35707000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr19:35694000-35704400	Enhancers	Primary T cells fromperipheralblood	blood
3	chr19:35694200-35708200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr19:35696600-35704600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:35696800-35704600	Weak transcription	Colonic Mucosa	Colon
6	chr19:35697400-35704600	Weak transcription	Small Intestine	intestine
7	chr19:35698000-35708200	Enhancers	Primary B cells from peripheral blood	blood
8	chr19:35698000-35708200	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr19:35698200-35708000	Enhancers	Primary B cells from cord blood	blood
10	chr19:35699200-35708000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:35700400-35704200	Enhancers	Primary T cells from cord blood	blood
12	chr19:35700600-35707200	Enhancers	Primary hematopoietic stem cells	blood
13	chr19:35701200-35709400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr19:35701400-35705600	Enhancers	Fetal Thymus	thymus
15	chr19:35702000-35704600	Weak transcription	Left Ventricle	heart
16	chr19:35702000-35704600	Weak transcription	K562	blood
17	chr19:35702000-35705000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:35702200-35706000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:35702400-35704600	Enhancers	GM12878-XiMat	blood
20	chr19:35702600-35704600	Enhancers	Duodenum Mucosa	Duodenum
21	chr19:35702600-35704600	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr19:35702800-35704600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr19:35702800-35705600	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr19:35703000-35704200	Weak transcription	Stomach Mucosa	stomach
25	chr19:35703000-35704600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr19:35703200-35704600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:35703200-35704600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:35703200-35704600	Weak transcription	Brain Anterior Caudate	brain
29	chr19:35703200-35707000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr19:35703400-35704400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr19:35703400-35704600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr19:35703400-35704600	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr19:35703400-35704600	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr19:35703400-35704600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr19:35703400-35704600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:35703400-35704600	Enhancers	Adipose Nuclei	Adipose
37	chr19:35703400-35704600	Weak transcription	Brain Hippocampus Middle	brain
38	chr19:35703400-35704600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr19:35703400-35704600	Weak transcription	Esophagus	oesophagus
40	chr19:35703400-35704600	Weak transcription	Lung	lung
41	chr19:35703400-35704600	Weak transcription	Right Atrium	heart
42	chr19:35703400-35704600	Weak transcription	Thymus	Thymus
43	chr19:35703400-35704600	Weak transcription	Spleen	Spleen
44	chr19:35703400-35705800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr19:35703600-35704200	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr19:35703600-35704600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr19:35703600-35704600	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr19:35703600-35704600	Weak transcription	Fetal Muscle Leg	muscle
49	chr19:35703600-35704600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr19:35703600-35704600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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