Variant report

Variant	rs12170215
Chromosome Location	chr22:27710440-27710441
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	chr22:27700594..27703155-chr22:27710130..27712224,2	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: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11090481	0.84[AFR][1000 genomes]
rs11090482	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11912637	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12165810	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12165996	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13056368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13056999	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13058409	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16984203	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1997645	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs483967	0.85[ASN][1000 genomes]
rs490925	0.86[ASN][1000 genomes]
rs570286	0.82[ASN][1000 genomes]
rs57851794	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71325232	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs71325233	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs71325235	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs713757	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs713818	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs736951	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8135866	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8137063	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8137296	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8139966	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8141513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8142278	0.99[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9306439	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9613422	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9613423	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9613424	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9620680	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9620683	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9620684	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9625199	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9625200	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:27705800-27710800	Enhancers	Ovary	ovary
2	chr22:27706800-27715400	Enhancers	Fetal Intestine Large	intestine
3	chr22:27707000-27710800	Enhancers	Rectal Mucosa Donor 29	rectum
4	chr22:27707200-27715400	Enhancers	Fetal Intestine Small	intestine
5	chr22:27707400-27710800	Enhancers	Adipose Nuclei	Adipose
6	chr22:27707400-27714600	Enhancers	Colonic Mucosa	Colon
7	chr22:27707800-27710600	Enhancers	Fetal Stomach	stomach
8	chr22:27708000-27710600	Enhancers	Brain Germinal Matrix	brain
9	chr22:27708200-27713400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr22:27708200-27715200	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr22:27708600-27712000	Enhancers	Pancreas	Pancrea
12	chr22:27708800-27710800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr22:27708800-27710800	Weak transcription	Spleen	Spleen
14	chr22:27709000-27714200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr22:27709000-27714600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr22:27709000-27715600	Enhancers	Fetal Brain Male	brain
17	chr22:27709200-27711000	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr22:27709200-27711400	Enhancers	K562	blood
19	chr22:27709200-27713600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr22:27709200-27714400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr22:27709400-27710600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr22:27709400-27711600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr22:27709400-27713200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr22:27709400-27713600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr22:27709400-27714200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr22:27709400-27714400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr22:27709400-27714600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr22:27709600-27713200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr22:27709600-27713400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr22:27709600-27713600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr22:27709800-27710800	Enhancers	Placenta Amnion	Placenta Amnion
32	chr22:27709800-27711400	Enhancers	Small Intestine	intestine
33	chr22:27709800-27712600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr22:27709800-27714600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr22:27710000-27710800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
36	chr22:27710000-27711000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr22:27710000-27711000	Enhancers	Stomach Mucosa	stomach
38	chr22:27710000-27712800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr22:27710000-27714000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr22:27710200-27710600	Weak transcription	Fetal Brain Female	brain
41	chr22:27710400-27710800	Active TSS	Duodenum Mucosa	Duodenum
42	chr22:27710400-27713400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr22:27710400-27713400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr22:27710400-27714200	Weak transcription	NH-A	brain
45	chr22:27710400-27714600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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