Variant report

Variant	rs2273522
Chromosome Location	chr14:31097345-31097346
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10130830	0.80[CHB][hapmap]
rs10131166	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10141944	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10142331	0.80[CHB][hapmap]
rs10146357	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10147257	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10149966	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1113946	0.88[CEU][hapmap];0.95[MEX][hapmap];0.81[AMR][1000 genomes]
rs11156637	0.83[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1123860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11622076	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11622786	0.83[AMR][1000 genomes]
rs11623154	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11625381	0.80[CHB][hapmap]
rs11627421	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11628700	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11846071	0.81[EUR][1000 genomes]
rs11846293	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11846408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11846420	0.83[CHD][hapmap]
rs11851205	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12434151	0.80[CHB][hapmap]
rs12586678	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12882048	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12882931	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12888568	0.88[CEU][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes]
rs12894186	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs142983	0.82[CEU][hapmap];0.86[AMR][1000 genomes]
rs17096941	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17097023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17097160	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs172946	0.80[CHB][hapmap]
rs2038451	0.87[CEU][hapmap]
rs2057284	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2070339	0.80[CHB][hapmap];0.83[CHD][hapmap]
rs2070340	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2273520	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2273521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs229144	0.80[CHB][hapmap]
rs229150	0.80[CHB][hapmap];0.83[CHD][hapmap]
rs229152	0.80[CHB][hapmap]
rs229154	0.80[CHB][hapmap]
rs229155	0.83[CHD][hapmap]
rs229161	0.80[CHB][hapmap]
rs229164	0.85[AMR][1000 genomes]
rs229190	0.80[CHB][hapmap]
rs229209	0.80[CHB][hapmap];0.85[CHD][hapmap]
rs229211	0.80[CHB][hapmap]
rs229244	0.86[CHB][hapmap];0.83[MEX][hapmap]
rs230340	0.80[CHB][hapmap];0.85[CHD][hapmap]
rs230351	0.80[CHB][hapmap];0.85[CHD][hapmap]
rs230364	0.80[CHB][hapmap]
rs230366	0.80[CHB][hapmap]
rs2378780	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs2378782	0.80[CHB][hapmap]
rs28567474	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs34935871	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35069045	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35389182	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3736773	0.88[CEU][hapmap];0.84[AMR][1000 genomes]
rs3825740	0.81[AMR][1000 genomes]
rs4430662	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs447853	0.81[MEX][hapmap];0.83[AMR][1000 genomes]
rs59856095	0.86[AMR][1000 genomes]
rs61976741	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6571356	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6571357	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6571361	0.80[CHB][hapmap]
rs7141333	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7141624	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7144204	0.85[CHD][hapmap]
rs7147530	0.80[CHB][hapmap]
rs7149113	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7153509	0.80[CHB][hapmap]
rs7154847	0.80[CHB][hapmap];0.88[CHD][hapmap]
rs7493549	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs761956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8006314	0.80[CHB][hapmap]
rs8008094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8009427	0.81[AMR][1000 genomes]
rs8012494	0.80[CHB][hapmap];0.85[CHD][hapmap]
rs8013017	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8015536	1.00[CHB][hapmap]
rs8018993	0.94[ASN][1000 genomes]
rs8019637	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9322864	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs9806111	0.80[CHB][hapmap];0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv564171	chr14:31068090-31149630	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2273522	SCFD1	cis	cerebellum	SCAN
rs2273522	G2E3	cis	parietal	SCAN
rs2273522	SCFD1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:31092200-31100200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr14:31092200-31104000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr14:31092200-31121000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr14:31092200-31133200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr14:31092200-31133200	Weak transcription	Esophagus	oesophagus
6	chr14:31092400-31099600	Weak transcription	Placenta	Placenta
7	chr14:31092400-31099800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr14:31092400-31100200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr14:31092400-31122800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr14:31092600-31100000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr14:31092800-31099600	Weak transcription	HSMM	muscle
12	chr14:31092800-31100000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr14:31092800-31102000	Weak transcription	Psoas Muscle	Psoas
14	chr14:31092800-31113200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr14:31092800-31114200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr14:31093000-31098200	Weak transcription	A549	lung
17	chr14:31093200-31100000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr14:31093400-31098800	Weak transcription	Fetal Intestine Small	intestine
19	chr14:31093400-31100200	Weak transcription	Fetal Intestine Large	intestine
20	chr14:31093400-31103800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr14:31093400-31103800	Weak transcription	Brain Hippocampus Middle	brain
22	chr14:31093600-31098400	Weak transcription	HMEC	breast
23	chr14:31093600-31099600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr14:31093600-31099600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr14:31093600-31099800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr14:31093600-31100000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr14:31093600-31100200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr14:31093600-31100600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr14:31093600-31101800	Weak transcription	HUVEC	blood vessel
30	chr14:31093600-31102000	Weak transcription	Fetal Kidney	kidney
31	chr14:31093600-31103800	Weak transcription	Brain Germinal Matrix	brain
32	chr14:31093600-31103800	Weak transcription	Fetal Lung	lung
33	chr14:31093600-31107200	Weak transcription	Right Ventricle	heart
34	chr14:31093600-31127200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr14:31093800-31098400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr14:31093800-31099800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr14:31093800-31100000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr14:31093800-31113800	Weak transcription	Brain Substantia Nigra	brain
39	chr14:31093800-31159600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr14:31094000-31097600	Strong transcription	Primary B cells from cord blood	blood
41	chr14:31094000-31098000	Weak transcription	NHDF-Ad	bronchial
42	chr14:31094000-31098200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr14:31094000-31099600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr14:31094000-31099600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr14:31094000-31100000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr14:31094000-31101600	Weak transcription	NH-A	brain
47	chr14:31094000-31101800	Weak transcription	Brain Angular Gyrus	brain
48	chr14:31094000-31111200	Weak transcription	HSMMtube	muscle
49	chr14:31094000-31113200	Weak transcription	Fetal Brain Male	brain
50	chr14:31094000-31122000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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