Variant report

Variant	rs229150
Chromosome Location	chr14:31099738-31099739
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:31098733..31102116-chr14:31103840..31105961,3	MCF-7	breast:
2	chr14:31090433..31092846-chr14:31098499..31101269,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000092108	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10130830	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10139154	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10142331	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10146357	0.80[CHB][hapmap];0.85[CHD][hapmap]
rs10147257	0.80[CHB][hapmap]
rs10147505	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1123860	0.80[CHB][hapmap]
rs11625381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11627421	0.80[CHB][hapmap];0.83[CHD][hapmap]
rs11628700	0.80[CHB][hapmap]
rs11846420	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12434151	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12882931	0.80[CHB][hapmap];0.85[CHD][hapmap]
rs151123	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs170663	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs170665	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs172946	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs179287	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs183467	0.86[EUR][1000 genomes]
rs1950882	0.98[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2045180	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2070339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2070340	0.80[CHB][hapmap];0.83[CHD][hapmap]
rs2273521	0.80[CHB][hapmap]
rs2273522	0.80[CHB][hapmap];0.83[CHD][hapmap]
rs229141	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs229143	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs229144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs229145	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs229152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229154	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229155	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229156	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs229161	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229162	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229171	0.86[EUR][1000 genomes]
rs229173	0.89[EUR][1000 genomes]
rs229176	0.89[EUR][1000 genomes]
rs229179	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs229184	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs229190	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs229194	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229195	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs229200	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs229201	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs229206	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229207	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs229209	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs229211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs229221	0.86[EUR][1000 genomes]
rs229222	0.83[EUR][1000 genomes]
rs229227	0.87[EUR][1000 genomes]
rs229228	0.85[EUR][1000 genomes]
rs229231	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs229235	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229236	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs229237	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs229240	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs229243	0.95[EUR][1000 genomes]
rs229244	0.85[ASW][hapmap]
rs229247	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs230340	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs230343	0.95[ASN][1000 genomes]
rs230351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs230353	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs230356	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs230360	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs230364	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs230366	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2378780	0.80[CHB][hapmap];0.87[CHD][hapmap]
rs2378781	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2378782	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34558066	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35069045	0.80[CHB][hapmap];0.83[CHD][hapmap]
rs35349033	0.83[ASN][1000 genomes]
rs4430662	0.80[CHB][hapmap];0.85[CHD][hapmap]
rs448175	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4981767	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4981770	0.84[CHB][hapmap];0.84[CHD][hapmap]
rs58049	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61976711	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6571361	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7141161	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7141333	0.80[CHB][hapmap]
rs7142948	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7144204	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7147530	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7152417	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7153509	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7153747	0.91[CEU][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs7154847	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7158351	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs761956	0.80[CHB][hapmap]
rs8006314	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs8008094	0.80[CHB][hapmap];0.85[CHD][hapmap]
rs8012494	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs8013017	0.80[CHB][hapmap]
rs8015536	0.80[CHB][hapmap]
rs9322864	0.80[CHB][hapmap];0.87[CHD][hapmap]
rs9806111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

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
rs229150	G2E3	cis	parietal	SCAN
rs229150	SCFD1	cis	parietal	SCAN
rs229150	SCFD1	cis	cerebellum	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	chr14:31092400-31099800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr14:31092400-31100200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr14:31092400-31122800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr14:31092600-31100000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr14:31092800-31100000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr14:31092800-31102000	Weak transcription	Psoas Muscle	Psoas
12	chr14:31092800-31113200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr14:31092800-31114200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr14:31093200-31100000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr14:31093400-31100200	Weak transcription	Fetal Intestine Large	intestine
16	chr14:31093400-31103800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr14:31093400-31103800	Weak transcription	Brain Hippocampus Middle	brain
18	chr14:31093600-31099800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr14:31093600-31100000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr14:31093600-31100200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr14:31093600-31100600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr14:31093600-31101800	Weak transcription	HUVEC	blood vessel
23	chr14:31093600-31102000	Weak transcription	Fetal Kidney	kidney
24	chr14:31093600-31103800	Weak transcription	Brain Germinal Matrix	brain
25	chr14:31093600-31103800	Weak transcription	Fetal Lung	lung
26	chr14:31093600-31107200	Weak transcription	Right Ventricle	heart
27	chr14:31093600-31127200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr14:31093800-31099800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr14:31093800-31100000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr14:31093800-31113800	Weak transcription	Brain Substantia Nigra	brain
31	chr14:31093800-31159600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr14:31094000-31100000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr14:31094000-31101600	Weak transcription	NH-A	brain
34	chr14:31094000-31101800	Weak transcription	Brain Angular Gyrus	brain
35	chr14:31094000-31111200	Weak transcription	HSMMtube	muscle
36	chr14:31094000-31113200	Weak transcription	Fetal Brain Male	brain
37	chr14:31094000-31122000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr14:31094200-31100000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr14:31094200-31111200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr14:31094200-31121000	Weak transcription	Spleen	Spleen
41	chr14:31094200-31145200	Weak transcription	Small Intestine	intestine
42	chr14:31094600-31101800	Weak transcription	Primary T cells from cord blood	blood
43	chr14:31094600-31104600	Weak transcription	Colon Smooth Muscle	Colon
44	chr14:31094600-31109200	Weak transcription	K562	blood
45	chr14:31094800-31100000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr14:31095200-31099800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr14:31095200-31100000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr14:31095200-31112400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr14:31095200-31119200	Weak transcription	Colonic Mucosa	Colon
50	chr14:31095400-31099800	Weak transcription	Fetal Thymus	thymus

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