Variant report

Variant	rs9322864
Chromosome Location	chr14:31196960-31196961
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:31189606..31191411-chr14:31195229..31197325,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000092108	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10130830	0.81[CHB][hapmap]
rs10131166	0.81[ASN][1000 genomes]
rs10136727	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10141944	0.81[ASN][1000 genomes]
rs10142331	0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs10146357	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs10147257	1.00[CHB][hapmap]
rs11156637	0.86[ASN][1000 genomes]
rs1123860	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11625381	0.81[CHB][hapmap]
rs11626600	0.90[CEU][hapmap];0.83[TSI][hapmap]
rs11627421	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[ASN][1000 genomes]
rs11628700	1.00[CHB][hapmap]
rs11846293	0.83[ASN][1000 genomes]
rs11846408	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs11846420	0.88[CHD][hapmap]
rs12434151	0.81[CHB][hapmap]
rs12586678	0.85[ASN][1000 genomes]
rs12882931	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs12894186	0.86[CHB][hapmap]
rs17096941	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs17097023	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs172946	0.81[CHB][hapmap]
rs2070339	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs2070340	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2273521	1.00[CHB][hapmap]
rs2273522	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs229144	0.81[CHB][hapmap]
rs229150	0.80[CHB][hapmap];0.87[CHD][hapmap]
rs229152	0.81[CHB][hapmap]
rs229154	0.81[CHB][hapmap]
rs229155	0.87[CHD][hapmap]
rs229161	0.81[CHB][hapmap]
rs229175	0.95[CEU][hapmap]
rs229190	0.81[CHB][hapmap]
rs229209	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs229211	0.81[CHB][hapmap]
rs229244	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs230340	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs230351	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs230364	0.81[CHB][hapmap]
rs230366	0.81[CHB][hapmap]
rs2378780	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2378781	0.82[EUR][1000 genomes]
rs2378782	0.81[CHB][hapmap];0.82[EUR][1000 genomes]
rs28567474	0.82[EUR][1000 genomes]
rs35069045	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[ASN][1000 genomes]
rs4430662	0.80[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs447853	0.90[CEU][hapmap]
rs61976741	1.00[ASN][1000 genomes]
rs6571361	0.81[CHB][hapmap]
rs7141333	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7144204	0.80[CHB][hapmap];0.85[CHD][hapmap]
rs7147530	0.81[CHB][hapmap];0.82[EUR][1000 genomes]
rs7153509	0.81[CHB][hapmap]
rs7154847	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs7493549	0.81[ASN][1000 genomes]
rs761956	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs8006314	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs8008094	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs8012494	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs8013017	1.00[CHB][hapmap]
rs8015536	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8018993	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9806111	0.81[CHB][hapmap];0.88[CHD][hapmap]

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
rs9322864	SCFD1	cis	parietal	SCAN
rs9322864	C14orf126	cis	cerebellum	SCAN
rs9322864	SCFD1	cis	cerebellum	SCAN
rs9322864	SCFD1	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 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	chr14:31133800-31197400	Weak transcription	Aorta	Aorta
6	chr14:31153600-31198800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr14:31160000-31206600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr14:31160000-31207200	Weak transcription	Right Ventricle	heart
9	chr14:31160400-31205000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr14:31160800-31197400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr14:31160800-31198600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr14:31160800-31206200	Weak transcription	Small Intestine	intestine
13	chr14:31161600-31197000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr14:31161800-31199000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr14:31162200-31199200	Strong transcription	HepG2	liver
16	chr14:31162400-31204000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr14:31165000-31208200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr14:31166000-31204200	Weak transcription	Colonic Mucosa	Colon
19	chr14:31166000-31205600	Weak transcription	Thymus	Thymus
20	chr14:31166400-31214200	Weak transcription	Pancreas	Pancrea
21	chr14:31168200-31205800	Weak transcription	Esophagus	oesophagus
22	chr14:31168200-31206000	Weak transcription	Gastric	stomach
23	chr14:31168200-31208600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr14:31171600-31205800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr14:31173600-31199200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr14:31177600-31205400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr14:31179000-31207400	Weak transcription	Fetal Kidney	kidney
28	chr14:31179200-31205200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr14:31179400-31197400	Weak transcription	Dnd41	blood
30	chr14:31180000-31205400	Weak transcription	NHLF	lung
31	chr14:31180800-31199000	Weak transcription	Fetal Intestine Small	intestine
32	chr14:31181600-31207000	Weak transcription	Hela-S3	cervix
33	chr14:31183800-31199000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr14:31184000-31199400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr14:31184400-31199000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr14:31185000-31199000	Strong transcription	Liver	Liver
37	chr14:31186000-31204000	Weak transcription	Brain Anterior Caudate	brain
38	chr14:31186400-31206200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr14:31190800-31197400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr14:31191000-31199400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr14:31191600-31199400	Strong transcription	Adipose Nuclei	Adipose
42	chr14:31192200-31198200	Strong transcription	Primary T cells from cord blood	blood
43	chr14:31192200-31199400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr14:31192200-31199400	Strong transcription	Duodenum Mucosa	Duodenum
45	chr14:31192400-31197600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr14:31192800-31204200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr14:31193000-31207200	Weak transcription	Brain Germinal Matrix	brain
48	chr14:31193000-31207800	Weak transcription	A549	lung
49	chr14:31193400-31199400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr14:31193600-31199400	Strong transcription	Primary B cells from cord blood	blood

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