Variant report

Variant	rs2838288
Chromosome Location	chr21:44783637-44783638
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:44781136..44783679-chr21:44846485..44848438,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CRYAA-2	chr21:44783212-44785567	XLOC_013961

Variant related genes	Relation type
ENSG00000142178	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs17004533	1.00[ASN][1000 genomes]
rs2838289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838291	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3746945	0.80[EUR][1000 genomes]
rs56914063	1.00[ASN][1000 genomes]
rs60618935	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61520171	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7279586	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7282956	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73378287	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73909444	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935798	1.00[ASN][1000 genomes]
rs935799	1.00[ASN][1000 genomes]
rs935800	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	nsv1056684	chr21:44539714-44886119	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv913831	chr21:44563995-44931821	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
3	esv1817359	chr21:44699077-44821595	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1057726	chr21:44711850-44957303	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv544466	chr21:44711850-44957303	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
6	nsv1058308	chr21:44722915-44825108	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1063186	chr21:44729904-44828476	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv544467	chr21:44729904-44828476	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv913837	chr21:44731138-44853859	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
10	nsv913838	chr21:44740134-44931821	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
11	nsv913839	chr21:44750200-44931821	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
12	nsv913840	chr21:44750643-44823479	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
13	nsv913841	chr21:44761874-44853859	Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
14	nsv913842	chr21:44764895-44792929	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv913843	chr21:44774757-44810756	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv913844	chr21:44779680-44875495	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
17	nsv913845	chr21:44781356-44874702	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
18	nsv470901	chr21:44781356-44884252	Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44777400-44788600	Enhancers	Fetal Brain Male	brain
2	chr21:44780200-44788400	Enhancers	Spleen	Spleen
3	chr21:44780800-44784800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr21:44781000-44784800	Weak transcription	Gastric	stomach
5	chr21:44781200-44783800	Enhancers	Primary hematopoietic stem cells	blood
6	chr21:44781200-44784000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr21:44781400-44785400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr21:44782000-44783800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
9	chr21:44782000-44783800	Enhancers	HSMMtube	muscle
10	chr21:44782200-44783800	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr21:44782200-44784000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr21:44782200-44791600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr21:44782400-44784400	Enhancers	Lung	lung
14	chr21:44782400-44784800	Weak transcription	Colonic Mucosa	Colon
15	chr21:44782400-44785000	Weak transcription	Pancreas	Pancrea
16	chr21:44782400-44785000	Weak transcription	Right Atrium	heart
17	chr21:44782400-44785400	Enhancers	Fetal Thymus	thymus
18	chr21:44782400-44789800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr21:44782600-44783800	Enhancers	Brain Germinal Matrix	brain
20	chr21:44782600-44783800	Enhancers	HSMM	muscle
21	chr21:44782600-44784800	Weak transcription	Fetal Intestine Large	intestine
22	chr21:44782600-44785200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr21:44782600-44785200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr21:44782600-44785600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr21:44782600-44785600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr21:44782600-44785600	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr21:44782600-44785800	Enhancers	Fetal Brain Female	brain
28	chr21:44782600-44787000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr21:44782600-44787000	Weak transcription	Brain Substantia Nigra	brain
30	chr21:44782600-44787800	Enhancers	Fetal Muscle Leg	muscle
31	chr21:44782600-44788800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr21:44782600-44790400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr21:44782800-44783800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr21:44782800-44783800	Enhancers	Duodenum Mucosa	Duodenum
35	chr21:44782800-44783800	Enhancers	GM12878-XiMat	blood
36	chr21:44782800-44784000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr21:44782800-44784200	Enhancers	Primary B cells from peripheral blood	blood
38	chr21:44782800-44784400	Weak transcription	Fetal Heart	heart
39	chr21:44782800-44784600	Weak transcription	Right Ventricle	heart
40	chr21:44782800-44785400	Weak transcription	Brain Hippocampus Middle	brain
41	chr21:44782800-44785600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr21:44782800-44787200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr21:44782800-44788600	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr21:44782800-44790000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr21:44783000-44783800	Enhancers	Primary T cells from cord blood	blood
46	chr21:44783000-44783800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr21:44783000-44783800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr21:44783000-44784200	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr21:44783000-44785000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr21:44783000-44785200	Weak transcription	Left Ventricle	heart

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