Variant report

Variant	rs554699
Chromosome Location	chr2:234761355-234761356
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234399142..234401068-chr2:234759873..234762356,2	MCF-7	breast:
2	chr2:234760939..234763453-chr2:235403879..235406192,2	K562	blood:
3	chr2:234759783..234762312-chr2:234875051..234877633,2	K562	blood:
4	chr2:234753471..234756128-chr2:234758714..234761959,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123485	Chromatin interaction
ENSG00000085982	Chromatin interaction
ENSG00000188042	Chromatin interaction
ENSG00000144481	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12692249	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs169922	0.87[ASN][1000 genomes]
rs169925	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs183331	0.88[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs213545	0.88[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs2286433	1.00[CEU][hapmap]
rs2302156	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs4663339	0.88[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs501145	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs503913	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap]
rs525359	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs528971	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs531643	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs556691	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs580045	1.00[CEU][hapmap];0.98[GIH][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs609942	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs619929	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs626110	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs637082	0.99[EUR][1000 genomes]
rs638071	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs6431643	0.88[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs6431644	0.87[ASN][1000 genomes]
rs648818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650570	0.97[EUR][1000 genomes]
rs650700	0.99[EUR][1000 genomes]
rs654279	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs689101	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7570755	0.91[CEU][hapmap]
rs887062	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv876023	chr2:234726154-234763137	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs554699	NCL	cis	parietal	SCAN
rs554699	CAB39	cis	parietal	SCAN
rs554699	SNORD20	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234736400-234762600	Weak transcription	Right Atrium	heart
2	chr2:234738200-234762000	Weak transcription	Esophagus	oesophagus
3	chr2:234740400-234762200	Weak transcription	Primary T cells from cord blood	blood
4	chr2:234741800-234762000	Weak transcription	Gastric	stomach
5	chr2:234742200-234762200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:234744000-234762400	Weak transcription	Small Intestine	intestine
7	chr2:234744600-234762000	Weak transcription	Colonic Mucosa	Colon
8	chr2:234748600-234762000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:234749200-234761600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:234750600-234761400	Weak transcription	Fetal Brain Female	brain
11	chr2:234752800-234761600	Weak transcription	Fetal Kidney	kidney
12	chr2:234753200-234761600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr2:234753200-234762200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:234756600-234762600	Transcr. at gene 5' and 3'	A549	lung
15	chr2:234756800-234762000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:234758400-234761600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:234758600-234762000	Weak transcription	Placenta	Placenta
18	chr2:234759000-234762600	Transcr. at gene 5' and 3'	Dnd41	blood
19	chr2:234759400-234761800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr2:234759600-234761800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:234760400-234762200	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr2:234760400-234762400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:234760400-234762400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
24	chr2:234760400-234763000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:234760600-234761400	Active TSS	NH-A	brain
26	chr2:234760600-234761400	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
27	chr2:234760600-234761600	Enhancers	Primary hematopoietic stem cells	blood
28	chr2:234760600-234761600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:234760600-234761600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:234760600-234761600	Genic enhancers	Fetal Muscle Leg	muscle
31	chr2:234760600-234761600	Transcr. at gene 5' and 3'	HepG2	liver
32	chr2:234760600-234761800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
33	chr2:234760600-234761800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:234760600-234761800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr2:234760600-234762000	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:234760600-234762000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:234760600-234762000	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
38	chr2:234760600-234762200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
39	chr2:234760600-234762400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:234760600-234762400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
41	chr2:234760600-234762400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr2:234760600-234762400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:234760600-234762400	Flanking Active TSS	Osteobl	bone
44	chr2:234760600-234762600	Flanking Active TSS	HUVEC	blood vessel
45	chr2:234760800-234761400	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr2:234760800-234761800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:234760800-234761800	Enhancers	Duodenum Mucosa	Duodenum
48	chr2:234760800-234762000	Enhancers	Fetal Lung	lung
49	chr2:234760800-234762200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
50	chr2:234760800-234762400	Transcr. at gene 5' and 3'	K562	blood

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