Variant report

Variant	rs2001998
Chromosome Location	chr14:69559518-69559519
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:69443330..69446418-chr14:69556824..69560512,4	MCF-7	breast:
2	chr14:69443630..69446372-chr14:69557045..69560333,4	MCF-7	breast:
3	chr14:69558940..69562138-chr14:69562200..69566674,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000072110	Chromatin interaction
ENSG00000259062	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1007407	0.82[JPT][hapmap]
rs10083451	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10130013	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10131077	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10132533	0.92[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap]
rs10134578	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10135102	0.81[AMR][1000 genomes]
rs10135127	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10135643	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10135971	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10139873	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10141040	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10143302	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10145565	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10146339	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10146649	0.89[EUR][1000 genomes]
rs10147369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10148614	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10149232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10151376	0.86[EUR][1000 genomes]
rs11158780	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11158782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158787	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11158790	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11158795	0.92[CEU][hapmap];0.89[CHB][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs11158798	0.92[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap]
rs1147481	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11622889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11628126	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs12323738	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12431846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12432970	0.85[JPT][hapmap]
rs12434478	0.85[JPT][hapmap]
rs12434775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12435594	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12437418	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12586650	0.83[GIH][hapmap]
rs12587583	0.83[GIH][hapmap]
rs12589028	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1275407	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1275415	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap]
rs12879406	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs12881049	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12885977	0.87[EUR][1000 genomes]
rs12886715	0.91[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap]
rs12889849	0.92[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap]
rs12891103	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12894822	0.83[GIH][hapmap]
rs17093668	0.85[JPT][hapmap]
rs1892296	0.88[EUR][1000 genomes]
rs1892297	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1914004	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2012764	0.82[JPT][hapmap]
rs2024892	0.84[JPT][hapmap]
rs2024893	0.85[JPT][hapmap]
rs2056153	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2268968	0.85[JPT][hapmap]
rs2300875	0.82[JPT][hapmap]
rs2331918	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs2331919	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28613298	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3211166	0.87[CEU][hapmap];0.89[CHB][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap]
rs35538328	0.84[EUR][1000 genomes]
rs4338726	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4899280	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs4902682	0.85[JPT][hapmap]
rs6573869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7144307	0.88[CEU][hapmap];0.91[GIH][hapmap]
rs7148045	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs7160629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8005658	0.82[AMR][1000 genomes]
rs8008184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8015876	0.85[JPT][hapmap]
rs8017103	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9323522	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9323524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[ASN][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	nsv832823	chr14:69388853-69567638	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2001998	SPTB	cis	cerebellum	SCAN
rs2001998	WDR22	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69522400-69564800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr14:69528600-69560200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr14:69535600-69565200	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr14:69540400-69560600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr14:69541400-69559800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr14:69542600-69570600	Strong transcription	Primary T cells from cord blood	blood
7	chr14:69546000-69563200	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr14:69546200-69583000	Weak transcription	Psoas Muscle	Psoas
9	chr14:69547200-69560400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr14:69548000-69560200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr14:69548000-69563000	Strong transcription	Fetal Thymus	thymus
12	chr14:69548000-69563600	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr14:69548200-69567400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr14:69548600-69560200	Weak transcription	Fetal Heart	heart
15	chr14:69548800-69559800	Weak transcription	A549	lung
16	chr14:69548800-69560200	Weak transcription	Stomach Mucosa	stomach
17	chr14:69550000-69568000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr14:69551600-69560200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr14:69554200-69560600	Weak transcription	Aorta	Aorta
20	chr14:69557600-69560000	Strong transcription	Ovary	ovary
21	chr14:69557800-69559600	Strong transcription	Fetal Intestine Small	intestine
22	chr14:69558000-69560400	Weak transcription	Pancreas	Pancrea
23	chr14:69558200-69563600	Weak transcription	Fetal Brain Male	brain
24	chr14:69558400-69559800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr14:69558400-69560000	Weak transcription	Colon Smooth Muscle	Colon
26	chr14:69558400-69560000	Weak transcription	NH-A	brain
27	chr14:69558600-69559800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr14:69558600-69559800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr14:69558600-69559800	Weak transcription	HMEC	breast
30	chr14:69558600-69560000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr14:69558600-69560000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr14:69558600-69560200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr14:69558600-69560200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr14:69558600-69560200	Weak transcription	Brain Anterior Caudate	brain
35	chr14:69558600-69560200	Weak transcription	Placenta	Placenta
36	chr14:69558600-69560200	Weak transcription	Right Ventricle	heart
37	chr14:69558600-69560400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr14:69558600-69560400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr14:69558600-69560400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr14:69558600-69560400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr14:69558600-69560400	Weak transcription	Fetal Stomach	stomach
42	chr14:69558600-69560600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr14:69558600-69560600	Weak transcription	Primary B cells from cord blood	blood
44	chr14:69558600-69560800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr14:69558600-69560800	Weak transcription	K562	blood
46	chr14:69558600-69561800	Weak transcription	Fetal Kidney	kidney
47	chr14:69558600-69564600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr14:69558600-69569600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr14:69558600-69570400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr14:69558600-69572000	Weak transcription	Brain Germinal Matrix	brain

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