Variant report

Variant	rs2878168
Chromosome Location	chr14:55320785-55320786
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:55318980..55321872-chr14:55325743..55328118,2	K562	blood:
2	chr14:55310463..55313127-chr14:55320351..55323154,2	MCF-7	breast:
3	chr14:55315509..55317878-chr14:55318793..55321643,2	MCF-7	breast:
4	chr14:55319568..55322164-chr14:55323468..55326255,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252019	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10131232	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs10133662	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs10133941	0.88[ASN][1000 genomes]
rs10483639	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11626298	0.90[ASN][1000 genomes]
rs11848732	0.89[ASN][1000 genomes]
rs12587434	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12589758	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17127992	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17128004	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2057368	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2057369	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2145945	0.84[ASN][1000 genomes]
rs2149483	0.98[ASN][1000 genomes]
rs4411417	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4462519	0.90[ASN][1000 genomes]
rs55985131	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57875940	0.97[EUR][1000 genomes]
rs58992937	0.85[EUR][1000 genomes]
rs59750960	0.83[EUR][1000 genomes]
rs60851395	0.82[EUR][1000 genomes]
rs67468157	0.96[ASN][1000 genomes]
rs7141685	0.84[ASN][1000 genomes]
rs7144602	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs7148266	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7151058	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7154323	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7155309	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72713453	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72713456	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72713460	0.93[EUR][1000 genomes]
rs72713467	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs752688	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8007201	1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs841	0.90[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9323272	0.84[ASN][1000 genomes]
rs9671371	0.87[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[YRI][hapmap];0.98[ASN][1000 genomes]
rs9671455	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9671850	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530042	chr14:55208170-55386966	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv819735	chr14:55319809-55326052	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2878168	CST9L	trans	cerebellum	SCAN
rs2878168	TXNDC16	cis	cerebellum	SCAN
rs2878168	FBXO34	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55303400-55337000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr14:55305200-55337200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr14:55305400-55325800	Weak transcription	Spleen	Spleen
4	chr14:55305800-55321000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr14:55305800-55326400	Weak transcription	Fetal Thymus	thymus
6	chr14:55306200-55320800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr14:55306200-55337000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr14:55306400-55336800	Weak transcription	Dnd41	blood
9	chr14:55306600-55321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr14:55306600-55336600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr14:55306800-55327400	Weak transcription	Pancreas	Pancrea
12	chr14:55306800-55337000	Weak transcription	Brain Anterior Caudate	brain
13	chr14:55308000-55336600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr14:55308200-55332400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr14:55308400-55330600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr14:55308600-55325600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr14:55308600-55325600	Weak transcription	Lung	lung
18	chr14:55309800-55320800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr14:55309800-55320800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr14:55309800-55321000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr14:55309800-55325600	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr14:55309800-55325800	Weak transcription	Thymus	Thymus
23	chr14:55311200-55325400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr14:55311800-55331200	Weak transcription	Hela-S3	cervix
25	chr14:55311800-55337000	Weak transcription	Fetal Intestine Large	intestine
26	chr14:55312800-55324800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr14:55313000-55322800	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr14:55313000-55325600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr14:55313000-55325800	Weak transcription	Gastric	stomach
30	chr14:55313200-55320800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr14:55313200-55321000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr14:55313200-55322800	Weak transcription	Fetal Intestine Small	intestine
33	chr14:55313200-55324200	Weak transcription	Primary T cells from cord blood	blood
34	chr14:55313400-55320800	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr14:55313600-55321000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr14:55314200-55322600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr14:55319600-55324000	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr14:55319600-55324800	Weak transcription	HepG2	liver
39	chr14:55320200-55321600	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr14:55320200-55321600	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr14:55320200-55322000	Enhancers	Primary B cells from peripheral blood	blood
42	chr14:55320200-55322800	Weak transcription	Liver	Liver
43	chr14:55320400-55321000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr14:55320400-55321000	Enhancers	Stomach Mucosa	stomach
45	chr14:55320400-55321200	Enhancers	H1 Cell Line	embryonic stem cell
46	chr14:55320400-55321400	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr14:55320400-55321600	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr14:55320400-55322000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr14:55320400-55323800	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr14:55320600-55321200	Enhancers	GM12878-XiMat	blood

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