Variant report

Variant	rs663258
Chromosome Location	chr3:42594019-42594020
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42586339..42588894-chr3:42591733..42594532,2	MCF-7	breast:
2	chr3:42592809..42595193-chr3:42597636..42599340,2	K562	blood:
3	chr3:42592301..42594170-chr3:42795995..42797942,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs13064311	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13066173	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066333	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs168138	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs171057	0.92[ASN][1000 genomes]
rs2068278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271181	0.97[ASN][1000 genomes]
rs2271184	0.94[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271187	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]
rs2284305	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs237064	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940407	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3095258	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.84[ASN][1000 genomes]
rs339656	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs339720	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs339721	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs339724	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs339729	0.88[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs339735	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs342523	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs342524	0.94[ASN][1000 genomes]
rs342525	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs342526	0.96[ASN][1000 genomes]
rs342534	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342535	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs342538	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383937	0.90[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs3888651	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs398743	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60994254	0.82[ASN][1000 genomes]
rs612362	0.90[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs637852	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs638904	0.85[ASN][1000 genomes]
rs651180	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.84[ASN][1000 genomes]
rs654761	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs664813	0.90[EUR][1000 genomes]
rs665206	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6799021	0.90[ASN][1000 genomes]
rs704982	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs807863	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs82755	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9311323	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9311324	0.94[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];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9813479	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9819563	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9828279	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	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
rs663258	SEC22C	Cis_1M	lymphoblastoid	RTeQTL
rs663258	NKTR	cis	cerebellum	SCAN
rs663258	NKTR	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42575200-42594400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:42577800-42597600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:42581800-42594400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:42582000-42594400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr3:42582200-42594400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:42586200-42595000	Weak transcription	Fetal Brain Male	brain
7	chr3:42586400-42594400	Weak transcription	NHEK	skin
8	chr3:42587000-42594200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:42587000-42594200	Weak transcription	HSMMtube	muscle
10	chr3:42587000-42594400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:42587000-42602400	Weak transcription	Colonic Mucosa	Colon
12	chr3:42587400-42597000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:42587400-42597200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:42587400-42606800	Weak transcription	Small Intestine	intestine
15	chr3:42587600-42594400	Weak transcription	HepG2	liver
16	chr3:42587800-42597000	Strong transcription	Fetal Thymus	thymus
17	chr3:42587800-42597000	Strong transcription	Thymus	Thymus
18	chr3:42587800-42611800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:42588000-42613000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:42588400-42613000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:42588600-42618000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:42589000-42594200	Weak transcription	NHDF-Ad	bronchial
23	chr3:42589000-42594600	Weak transcription	HSMM	muscle
24	chr3:42589000-42611800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr3:42589200-42611000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:42589400-42594200	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:42589400-42594400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:42589400-42595400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:42589400-42596800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:42589400-42610800	Weak transcription	Stomach Mucosa	stomach
31	chr3:42589400-42611000	Strong transcription	Fetal Stomach	stomach
32	chr3:42589400-42612400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:42589400-42614000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr3:42589600-42611200	Strong transcription	Fetal Intestine Small	intestine
35	chr3:42589600-42611800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr3:42589800-42595800	Strong transcription	Primary T cells from cord blood	blood
37	chr3:42589800-42597000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:42589800-42597000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:42589800-42597200	Weak transcription	Hela-S3	cervix
40	chr3:42589800-42610600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:42589800-42611000	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr3:42589800-42616400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr3:42590000-42597000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:42590000-42597800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:42590000-42598600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:42590000-42603800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:42590000-42611600	Strong transcription	Duodenum Mucosa	Duodenum
48	chr3:42590000-42612600	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr3:42590200-42601600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:42590200-42611600	Strong transcription	Fetal Muscle Leg	muscle

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