Variant report

Variant	rs5997220
Chromosome Location	chr22:27709560-27709561
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	chr22:27707736..27710195-chr22:27719270..27720776,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CRYBA4-8	chr22:27706612-27711010	XLOC_014197
2	lnc-CRYBA4-8	chr22:27706612-27711010	ENSG00000226741

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1106715	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1607498	0.92[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16984292	0.87[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2176659	0.82[MEX][hapmap]
rs35173189	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs513674	0.85[CEU][hapmap]
rs55759797	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55826249	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56676248	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61289506	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8135463	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8135561	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8141118	0.84[ASN][1000 genomes]
rs9608598	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9613418	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413125	chr22:27404463-28121577	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv459860	chr22:27527005-28181436	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv588872	chr22:27527005-28181436	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv834166	chr22:27628570-27814359	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv3359531	chr22:27706552-27710850	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5997220	TTC28AS	cis	parietal	SCAN
rs5997220	NF2	cis	parietal	SCAN
rs5997220	SLC6A4	trans	lymphoblastoid	seeQTL
rs5997220	RAB27A	trans	lymphoblastoid	seeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:27705800-27710800	Enhancers	Ovary	ovary
2	chr22:27706000-27709600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr22:27706800-27715400	Enhancers	Fetal Intestine Large	intestine
4	chr22:27707000-27710200	Enhancers	Duodenum Mucosa	Duodenum
5	chr22:27707000-27710800	Enhancers	Rectal Mucosa Donor 29	rectum
6	chr22:27707200-27710400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr22:27707200-27715400	Enhancers	Fetal Intestine Small	intestine
8	chr22:27707400-27710000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr22:27707400-27710800	Enhancers	Adipose Nuclei	Adipose
10	chr22:27707400-27714600	Enhancers	Colonic Mucosa	Colon
11	chr22:27707600-27709600	Enhancers	Primary hematopoietic stem cells	blood
12	chr22:27707600-27709800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr22:27707600-27710400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr22:27707800-27709600	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr22:27707800-27709800	Enhancers	Osteobl	bone
16	chr22:27707800-27710600	Enhancers	Fetal Stomach	stomach
17	chr22:27708000-27710000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr22:27708000-27710400	Enhancers	Aorta	Aorta
19	chr22:27708000-27710600	Enhancers	Brain Germinal Matrix	brain
20	chr22:27708200-27709600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr22:27708200-27709600	Enhancers	Fetal Muscle Leg	muscle
22	chr22:27708200-27709800	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr22:27708200-27709800	Weak transcription	Small Intestine	intestine
24	chr22:27708200-27710200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr22:27708200-27713400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr22:27708200-27715200	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr22:27708400-27709600	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr22:27708400-27710200	Enhancers	Fetal Brain Female	brain
29	chr22:27708600-27709800	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr22:27708600-27712000	Enhancers	Pancreas	Pancrea
31	chr22:27708800-27709600	Enhancers	Brain Anterior Caudate	brain
32	chr22:27708800-27709800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr22:27708800-27710000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr22:27708800-27710200	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr22:27708800-27710800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr22:27708800-27710800	Weak transcription	Spleen	Spleen
37	chr22:27709000-27709600	Enhancers	H1 Cell Line	embryonic stem cell
38	chr22:27709000-27709600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr22:27709000-27709800	Enhancers	NH-A	brain
40	chr22:27709000-27710000	Weak transcription	Right Atrium	heart
41	chr22:27709000-27710200	Weak transcription	Lung	lung
42	chr22:27709000-27710400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr22:27709000-27714200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr22:27709000-27714600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr22:27709000-27715600	Enhancers	Fetal Brain Male	brain
46	chr22:27709200-27711000	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr22:27709200-27711400	Enhancers	K562	blood
48	chr22:27709200-27713600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr22:27709200-27714400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr22:27709400-27710400	Enhancers	Fetal Kidney	kidney

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