Variant report

Variant	rs229355
Chromosome Location	chr21:44871682-44871683
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:44582262..44583964-chr21:44870568..44872491,2	MCF-7	breast:
2	chr21:44870036..44872760-chr21:44874681..44876370,2	MCF-7	breast:
3	chr21:44865967..44867477-chr21:44871611..44873859,2	K562	blood:
4	chr21:44870502..44872500-chr21:44876029..44877789,2	MCF-7	breast:
5	chr21:44870027..44872296-chr21:44872310..44874913,2	MCF-7	breast:
6	chr21:44871086..44873252-chr21:44875393..44877647,3	K562	blood:
7	chr21:44870566..44873425-chr21:44917940..44920112,2	MCF-7	breast:

(count:6 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RRP1B-3	chr21:44871053-44872385	XLOC_013964
2	lnc-RRP1B-3	chr21:44871053-44873773	XLOC_013964
3	lnc-RRP1B-3	chr21:44871053-44872385	ENSG00000188660
4	lnc-RRP1B-3	chr21:44871053-44872385	NONHSAT082407
5	lnc-RRP1B-3	chr21:44871053-44872385	NR_026960
6	lnc-RRP1B-3	chr21:44871053-44873765	NONHSAT082409

No data

Variant related genes	Relation type
ENSG00000188660	Chromatin interaction
ENSG00000228120	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17004554	0.82[YRI][hapmap]
rs17004555	0.82[YRI][hapmap]
rs1865758	0.84[YRI][hapmap]
rs2838303	0.89[JPT][hapmap]
rs6518212	0.82[YRI][hapmap]
rs8131995	0.82[YRI][hapmap]
rs9647237	0.82[YRI][hapmap]
rs9982011	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:33 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv913847	chr21:44792003-44931821	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
11	nsv913849	chr21:44817248-44925334	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
12	nsv516339	chr21:44823479-44873060	Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
13	nsv913852	chr21:44829087-44925334	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
14	nsv913853	chr21:44831981-44873017	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
15	nsv913854	chr21:44831981-44873060	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
16	nsv913855	chr21:44831981-44873795	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
17	nsv913856	chr21:44831981-44874702	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
18	nsv913857	chr21:44831981-44875495	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
19	nsv913858	chr21:44831981-44877881	Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
20	nsv913859	chr21:44831981-44884252	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
21	nsv913860	chr21:44831981-44925334	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS 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	95 gene(s)	inside rSNPs	diseases
22	nsv913862	chr21:44833854-44877881	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
23	nsv913865	chr21:44835508-44873017	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
24	nsv913866	chr21:44835508-44874702	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
25	nsv913867	chr21:44835508-44925334	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
26	nsv913868	chr21:44835508-44954522	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
27	nsv828901	chr21:44838108-44873453	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
28	nsv913870	chr21:44848070-44875495	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
29	nsv913871	chr21:44858534-44874702	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
30	nsv587687	chr21:44860542-44874702	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
31	nsv913872	chr21:44860542-44925334	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
32	nsv587688	chr21:44864079-44874702	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
33	esv1839560	chr21:44864079-44973184	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs229355	KRTAP12-3	cis	cerebellum	SCAN
rs229355	KRTAP10-1	cis	parietal	SCAN
rs229355	NCRNA00175	cis	cerebellum	SCAN
rs229355	AIRE	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44856800-44873200	Enhancers	Placenta	Placenta
2	chr21:44859400-44883600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr21:44863400-44877200	Weak transcription	Right Atrium	heart
4	chr21:44865000-44873800	Weak transcription	GM12878-XiMat	blood
5	chr21:44866200-44873400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr21:44866600-44872200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
7	chr21:44867000-44881000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr21:44868000-44872200	Enhancers	Fetal Thymus	thymus
9	chr21:44868400-44876000	Weak transcription	Left Ventricle	heart
10	chr21:44868600-44878400	Enhancers	Fetal Brain Male	brain
11	chr21:44869000-44873200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr21:44869200-44874200	Enhancers	Fetal Brain Female	brain
13	chr21:44869400-44872000	Enhancers	Fetal Stomach	stomach
14	chr21:44869600-44873200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr21:44869600-44873200	Enhancers	Fetal Lung	lung
16	chr21:44869600-44873200	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr21:44869800-44872200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr21:44869800-44872200	Enhancers	Muscle Satellite Cultured Cells	--
19	chr21:44869800-44873000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr21:44869800-44873000	Enhancers	Esophagus	oesophagus
21	chr21:44869800-44873400	Enhancers	HMEC	breast
22	chr21:44870000-44872200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr21:44870000-44873000	Enhancers	NHEK	skin
24	chr21:44870400-44876200	Weak transcription	Fetal Intestine Small	intestine
25	chr21:44870800-44871800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr21:44870800-44872600	Enhancers	Placenta Amnion	Placenta Amnion
27	chr21:44870800-44873800	Weak transcription	Thymus	Thymus
28	chr21:44870800-44880600	Weak transcription	HepG2	liver
29	chr21:44871000-44871800	Flanking Active TSS	HSMM	muscle
30	chr21:44871000-44872400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr21:44871000-44872800	Weak transcription	Right Ventricle	heart
32	chr21:44871000-44873000	Enhancers	NH-A	brain
33	chr21:44871000-44882800	Weak transcription	Brain Germinal Matrix	brain
34	chr21:44871200-44872000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr21:44871200-44872000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
36	chr21:44871400-44872000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr21:44871400-44872400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr21:44871400-44873200	Weak transcription	Stomach Mucosa	stomach
39	chr21:44871400-44873200	Enhancers	A549	lung
40	chr21:44871400-44874800	Weak transcription	Lung	lung
41	chr21:44871400-44875400	Weak transcription	Fetal Heart	heart
42	chr21:44871600-44872000	Enhancers	Osteobl	bone
43	chr21:44871600-44872400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr21:44871600-44872400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr21:44871600-44873200	Enhancers	HSMMtube	muscle

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