Variant report

Variant	rs2271187
Chromosome Location	chr3:42610515-42610516
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42609124..42614031-chr3:42620291..42625613,5	MCF-7	breast:
2	chr3:42607223..42608765-chr3:42608962..42611402,2	MCF-7	breast:
3	chr3:42609334..42611194-chr3:42617975..42620202,2	K562	blood:
4	chr3:42610241..42612641-chr3:42709533..42711568,2	K562	blood:

Variant related genes	Relation type
ENSG00000093183	Chromatin interaction
ENSG00000008324	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs13064311	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13066173	0.83[ASW][hapmap];0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13066333	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs168138	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs171057	0.87[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2068278	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2271181	0.88[ASN][1000 genomes]
rs2271184	0.83[ASW][hapmap];0.81[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2284305	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs237064	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2940407	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095258	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs339656	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[ASN][1000 genomes]
rs339720	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs339721	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[ASN][1000 genomes]
rs339724	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs339729	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[ASN][1000 genomes]
rs339735	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs342523	0.95[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs342524	0.82[ASN][1000 genomes]
rs342526	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs342534	0.88[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs342535	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs342538	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs383937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3888651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs398743	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[ASN][1000 genomes]
rs60994254	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs612362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs637852	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs638904	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs651180	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs654761	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs663258	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs664813	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs665206	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs704982	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs807863	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs82755	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[ASN][1000 genomes]
rs9311323	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9311324	0.83[ASW][hapmap];0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9813479	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9819563	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828279	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[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	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2271187	NKTR	cis	parietal	SCAN
rs2271187	SEC22C	Cis_1M	lymphoblastoid	RTeQTL
rs2271187	NKTR	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42587800-42611800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:42588000-42613000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:42588400-42613000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:42588600-42618000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:42589000-42611800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:42589200-42611000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:42589400-42610800	Weak transcription	Stomach Mucosa	stomach
8	chr3:42589400-42611000	Strong transcription	Fetal Stomach	stomach
9	chr3:42589400-42612400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:42589400-42614000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:42589600-42611200	Strong transcription	Fetal Intestine Small	intestine
12	chr3:42589600-42611800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr3:42589800-42610600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:42589800-42611000	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:42589800-42616400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:42590000-42611600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr3:42590000-42612600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr3:42590200-42611600	Strong transcription	Fetal Muscle Leg	muscle
19	chr3:42590200-42611800	Strong transcription	Adipose Nuclei	Adipose
20	chr3:42591000-42614000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:42591200-42611800	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:42591400-42611200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:42591600-42611800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:42591800-42610600	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr3:42592000-42611800	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:42592800-42610600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:42593400-42611000	Strong transcription	Liver	Liver
28	chr3:42593400-42612000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr3:42593600-42611600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:42593800-42611600	Strong transcription	Fetal Brain Female	brain
31	chr3:42594400-42611600	Strong transcription	Stomach Smooth Muscle	stomach
32	chr3:42594600-42615200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr3:42594800-42610800	Weak transcription	Fetal Heart	heart
34	chr3:42598000-42611400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:42598000-42615600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:42598200-42611000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:42598200-42616400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:42598400-42611800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:42598600-42611600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:42598600-42612800	Strong transcription	Fetal Thymus	thymus
41	chr3:42599600-42612200	Strong transcription	Dnd41	blood
42	chr3:42599800-42611000	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr3:42599800-42611400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr3:42600000-42611600	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:42600200-42611800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:42600400-42611800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr3:42600800-42611400	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:42601400-42611800	Strong transcription	Thymus	Thymus
49	chr3:42601800-42610600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr3:42602400-42611800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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