Variant report

Variant	rs17097160
Chromosome Location	chr14:31202740-31202741
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr14:31202711-31202771	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:31202299..31203041-chr20:44440585..44441167,2	MCF-7	breast:

Variant related genes	Relation type
SCFD1	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10146357	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs10147257	0.88[CEU][hapmap]
rs1113946	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap]
rs1123860	0.88[CEU][hapmap]
rs11622786	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11627421	0.88[CEU][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes]
rs11628700	0.83[CEU][hapmap]
rs11846408	0.88[CEU][hapmap]
rs12882931	0.88[CEU][hapmap];0.90[MEX][hapmap]
rs12888568	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12894186	0.88[CEU][hapmap]
rs142983	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs17096941	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs17097023	0.88[CEU][hapmap]
rs17097130	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2038451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2070340	0.83[CEU][hapmap];0.83[MEX][hapmap]
rs2273521	0.88[CEU][hapmap]
rs2273522	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs229164	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35069045	0.88[CEU][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes]
rs3736773	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4399466	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4430662	0.83[CEU][hapmap];0.83[MEX][hapmap]
rs447853	0.84[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs61976712	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61976741	0.84[AMR][1000 genomes]
rs761956	0.88[CEU][hapmap];0.85[AMR][1000 genomes]
rs8008094	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs8012325	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[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	nsv564169	chr14:30819087-31541494	Strong transcription Genic enhancers ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1036419	chr14:30969616-31224226	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv901581	chr14:30978745-31585289	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17097160	SCFD1	cis	parietal	SCAN
rs17097160	G2E3	cis	parietal	SCAN
rs17097160	SCFD1	cis	multi-tissue	Pritchard
rs17097160	SCFD1	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:31113800-31205400	Weak transcription	Fetal Brain Male	brain
2	chr14:31122800-31205200	Weak transcription	Brain Angular Gyrus	brain
3	chr14:31123000-31212000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr14:31123400-31216400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr14:31160000-31206600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr14:31160000-31207200	Weak transcription	Right Ventricle	heart
7	chr14:31160400-31205000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr14:31160800-31206200	Weak transcription	Small Intestine	intestine
9	chr14:31162400-31204000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr14:31165000-31208200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr14:31166000-31204200	Weak transcription	Colonic Mucosa	Colon
12	chr14:31166000-31205600	Weak transcription	Thymus	Thymus
13	chr14:31166400-31214200	Weak transcription	Pancreas	Pancrea
14	chr14:31168200-31205800	Weak transcription	Esophagus	oesophagus
15	chr14:31168200-31206000	Weak transcription	Gastric	stomach
16	chr14:31168200-31208600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr14:31171600-31205800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr14:31177600-31205400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr14:31179000-31207400	Weak transcription	Fetal Kidney	kidney
20	chr14:31179200-31205200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr14:31180000-31205400	Weak transcription	NHLF	lung
22	chr14:31181600-31207000	Weak transcription	Hela-S3	cervix
23	chr14:31186000-31204000	Weak transcription	Brain Anterior Caudate	brain
24	chr14:31186400-31206200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr14:31192800-31204200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr14:31193000-31207200	Weak transcription	Brain Germinal Matrix	brain
27	chr14:31193000-31207800	Weak transcription	A549	lung
28	chr14:31196000-31207400	Weak transcription	Colon Smooth Muscle	Colon
29	chr14:31196000-31208800	Weak transcription	HUVEC	blood vessel
30	chr14:31196200-31208600	Weak transcription	Spleen	Spleen
31	chr14:31196400-31208400	Weak transcription	Lung	lung
32	chr14:31196400-31216800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr14:31197000-31204200	Weak transcription	HSMMtube	muscle
34	chr14:31197200-31202800	Weak transcription	Fetal Lung	lung
35	chr14:31197200-31202800	Weak transcription	Fetal Thymus	thymus
36	chr14:31197200-31204200	Weak transcription	Left Ventricle	heart
37	chr14:31197200-31205200	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr14:31197400-31204000	Weak transcription	Brain Hippocampus Middle	brain
39	chr14:31197600-31204000	Weak transcription	HMEC	breast
40	chr14:31197600-31207800	Weak transcription	K562	blood
41	chr14:31197600-31208000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr14:31197800-31203000	Weak transcription	Placenta	Placenta
43	chr14:31197800-31205200	Weak transcription	NHEK	skin
44	chr14:31197800-31207000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr14:31198000-31204000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr14:31198000-31204200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr14:31198000-31205200	Weak transcription	Fetal Heart	heart
48	chr14:31198200-31202800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr14:31198200-31206000	Weak transcription	Aorta	Aorta
50	chr14:31199000-31203400	Weak transcription	NHDF-Ad	bronchial

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