Variant report

Variant	rs17673930
Chromosome Location	chr14:55808151-55808152
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	chr14:55738126..55740346-chr14:55806571..55808200,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258413	Chromatin interaction
ENSG00000178974	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10483641	0.89[CEU][hapmap]
rs10498475	1.00[CEU][hapmap];0.80[AMR][1000 genomes]
rs17128484	0.82[CEU][hapmap]
rs17671923	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17672376	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17672950	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17675052	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17740413	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17741681	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17741825	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17742621	0.80[CEU][hapmap];1.00[CHD][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17743484	0.89[CEU][hapmap];1.00[CHD][hapmap]
rs1959443	0.89[CEU][hapmap];1.00[CHD][hapmap]
rs2274271	0.89[CEU][hapmap]
rs35070799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41299199	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41437744	0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[AFR][1000 genomes]
rs60505634	1.00[ASN][1000 genomes]
rs6573008	0.80[CEU][hapmap];0.91[TSI][hapmap]
rs713473	0.89[CEU][hapmap];1.00[CHD][hapmap]
rs713475	0.89[CEU][hapmap];1.00[CHD][hapmap]
rs7141706	1.00[CEU][hapmap]
rs7159490	0.89[CEU][hapmap];0.84[TSI][hapmap]
rs7160411	1.00[CEU][hapmap]
rs72717745	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72717751	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72717752	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72717759	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9323280	0.86[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039438	chr14:55746585-55886099	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17673930	SOCS4	cis	multi-tissue	Pritchard
rs17673930	FBXO34	cis	cerebellum	SCAN
rs17673930	KTN1	cis	multi-tissue	Pritchard
rs17673930	MAPK1IP1L	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55779200-55817600	Weak transcription	Hela-S3	cervix
2	chr14:55780800-55817200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr14:55782000-55817200	Weak transcription	HSMM	muscle
4	chr14:55791800-55817200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr14:55793000-55808600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr14:55794000-55811800	Weak transcription	Brain Anterior Caudate	brain
7	chr14:55798200-55817200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr14:55800000-55817200	Weak transcription	Dnd41	blood
9	chr14:55800600-55816200	Weak transcription	Primary B cells from cord blood	blood
10	chr14:55800600-55823600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr14:55801000-55808400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr14:55801000-55808600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr14:55801000-55817200	Weak transcription	HepG2	liver
14	chr14:55801200-55817200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr14:55801200-55817200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr14:55801200-55817200	Weak transcription	Liver	Liver
17	chr14:55801200-55817200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr14:55801200-55842800	Weak transcription	Fetal Brain Male	brain
19	chr14:55801400-55817400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr14:55801400-55817400	Weak transcription	Brain Hippocampus Middle	brain
21	chr14:55801600-55817200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr14:55802200-55817000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr14:55802200-55817400	Weak transcription	Fetal Intestine Small	intestine
24	chr14:55803200-55808200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr14:55803200-55809000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr14:55803400-55809200	Weak transcription	Colonic Mucosa	Colon
27	chr14:55803400-55817200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr14:55803400-55817200	Weak transcription	Placenta	Placenta
29	chr14:55803600-55817200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr14:55804400-55811000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr14:55804600-55808800	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr14:55804800-55811400	Weak transcription	Gastric	stomach
33	chr14:55805200-55811800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr14:55805200-55813600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr14:55805200-55817200	Weak transcription	Fetal Intestine Large	intestine
36	chr14:55805400-55808200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr14:55805400-55810400	Weak transcription	Stomach Mucosa	stomach
38	chr14:55805400-55812200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr14:55805800-55808200	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr14:55805800-55817600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr14:55806200-55809400	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr14:55806400-55808200	Enhancers	Right Ventricle	heart
43	chr14:55806600-55808200	Enhancers	Left Ventricle	heart
44	chr14:55806600-55808200	Enhancers	Psoas Muscle	Psoas
45	chr14:55806600-55808800	Enhancers	Small Intestine	intestine
46	chr14:55806600-55811000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr14:55806600-55817000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr14:55806800-55810400	Weak transcription	K562	blood
49	chr14:55806800-55815600	Weak transcription	Fetal Kidney	kidney
50	chr14:55806800-55820800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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