Variant report

Variant	rs3095258
Chromosome Location	chr3:42659903-42659904
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr3:42659682-42659925	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:42588038..42590456-chr3:42657625..42660579,3	K562	blood:
2	chr3:42659807..42662376-chr3:42694804..42697042,2	MCF-7	breast:
3	chr3:42659157..42660714-chr3:42671631..42673408,2	K562	blood:

Variant related genes	Relation type
NKTR	TF binding region
ENSG00000114857	Chromatin interaction
ENSG00000114853	Chromatin interaction
ENSG00000230084	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs13064311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13066173	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.84[ASN][1000 genomes]
rs13066333	0.83[ASN][1000 genomes]
rs168138	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2068278	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]
rs2271181	0.84[ASN][1000 genomes]
rs2271184	0.81[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];0.85[ASN][1000 genomes]
rs2271187	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]
rs2284305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs237064	0.84[ASN][1000 genomes]
rs2940407	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs339656	0.83[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339720	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs339721	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs339724	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs339729	0.83[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs339735	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342523	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]
rs342534	0.88[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs342535	0.82[ASN][1000 genomes]
rs342538	0.84[ASN][1000 genomes]
rs383937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3888651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs398743	0.83[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60994254	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs612362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs637852	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs638904	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs651180	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs654761	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs663258	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]
rs664813	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs665206	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs704982	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs807863	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs82755	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9311323	0.90[ASN][1000 genomes]
rs9311324	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9813479	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9819563	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9828279	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[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	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
2	nsv876730	chr3:42643935-42667936	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3095258	NKTR	cis	cerebellum	SCAN
rs3095258	NKTR	cis	parietal	SCAN
rs3095258	SNRK	cis	cerebellum	SCAN
rs3095258	SEC22C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42643200-42672800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:42643600-42675000	Weak transcription	Aorta	Aorta
3	chr3:42643800-42671200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:42644000-42660000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:42644000-42671000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:42644000-42671200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:42644000-42671400	Weak transcription	HSMMtube	muscle
8	chr3:42644000-42672000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:42644200-42663200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:42644200-42672400	Weak transcription	Fetal Kidney	kidney
11	chr3:42644800-42660000	Weak transcription	Colonic Mucosa	Colon
12	chr3:42644800-42660200	Weak transcription	NH-A	brain
13	chr3:42645200-42660200	Weak transcription	HMEC	breast
14	chr3:42646000-42672000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:42647000-42671400	Weak transcription	NHEK	skin
16	chr3:42647200-42668600	Weak transcription	Brain Germinal Matrix	brain
17	chr3:42647200-42688200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr3:42647400-42672000	Weak transcription	NHLF	lung
19	chr3:42647600-42672000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:42647600-42677600	Weak transcription	Gastric	stomach
21	chr3:42648800-42672600	Weak transcription	Fetal Brain Female	brain
22	chr3:42649800-42671200	Weak transcription	Fetal Brain Male	brain
23	chr3:42650200-42660000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr3:42650400-42660000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:42650400-42660000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:42650400-42660200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:42650400-42660600	Weak transcription	Fetal Heart	heart
28	chr3:42650400-42671400	Weak transcription	Thymus	Thymus
29	chr3:42650400-42671800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:42650400-42672000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:42650600-42660000	Weak transcription	Fetal Lung	lung
32	chr3:42650600-42660400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:42650600-42669400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:42650600-42669400	Weak transcription	Fetal Muscle Leg	muscle
35	chr3:42650600-42672600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:42650600-42673000	Weak transcription	Esophagus	oesophagus
37	chr3:42650800-42660200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:42650800-42663200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:42650800-42672800	Weak transcription	Ovary	ovary
40	chr3:42651000-42660200	Weak transcription	Liver	Liver
41	chr3:42651000-42660200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr3:42651200-42693000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:42651400-42660200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:42651400-42671000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr3:42651800-42680400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:42652000-42660000	Weak transcription	NHDF-Ad	bronchial
47	chr3:42653000-42660000	Weak transcription	Fetal Intestine Large	intestine
48	chr3:42653000-42660000	Weak transcription	Placenta	Placenta
49	chr3:42653000-42660200	Weak transcription	HepG2	liver
50	chr3:42653200-42660200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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