Variant report

Variant	rs342508
Chromosome Location	chr3:42580706-42580707
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42574066..42576478-chr3:42578308..42581345,3	K562	blood:
2	chr3:42513786..42515650-chr3:42578967..42581599,2	MCF-7	breast:
3	chr3:42572313..42574603-chr3:42579698..42581562,2	MCF-7	breast:
4	chr3:42266384..42268171-chr3:42579135..42581399,2	MCF-7	breast:
5	chr3:42543347..42544924-chr3:42580025..42581850,2	K562	blood:

Variant related genes	Relation type
ENSG00000232354	Chromatin interaction
ENSG00000114812	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs171057	0.81[AMR][1000 genomes]
rs2136012	0.81[JPT][hapmap]
rs2271185	0.81[ASN][1000 genomes]
rs2271186	0.87[CHD][hapmap];0.81[JPT][hapmap]
rs2976533	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs339658	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs339726	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs339727	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs342507	0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs342521	0.86[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs342522	0.81[ASN][1000 genomes]
rs342536	0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs3774398	0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4549	0.84[CHD][hapmap]
rs607568	0.81[JPT][hapmap]
rs639692	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs640689	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs6441892	0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs663673	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs6799021	0.88[EUR][1000 genomes]
rs689251	0.81[JPT][hapmap]
rs8351	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs925457	0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529987	chr3:41921995-42591771	Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	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
3	esv1804804	chr3:42515186-42582403	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv1814102	chr3:42539966-42582403	Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	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
rs342508	NKTR	cis	cerebellum	SCAN
rs342508	NKTR	cis	parietal	SCAN
rs342508	SEC22C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42552200-42581000	Weak transcription	Pancreas	Pancrea
2	chr3:42557800-42586000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr3:42557800-42590400	Weak transcription	Aorta	Aorta
4	chr3:42558000-42585200	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:42561000-42581000	Weak transcription	Gastric	stomach
6	chr3:42562400-42586800	Weak transcription	Small Intestine	intestine
7	chr3:42570000-42580800	Weak transcription	Colonic Mucosa	Colon
8	chr3:42571200-42581200	Weak transcription	Right Atrium	heart
9	chr3:42571800-42581600	Weak transcription	Liver	Liver
10	chr3:42571800-42586200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:42572800-42581000	Weak transcription	Right Ventricle	heart
12	chr3:42573800-42580800	Weak transcription	Stomach Mucosa	stomach
13	chr3:42574600-42585000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:42574800-42585600	Weak transcription	Brain Anterior Caudate	brain
15	chr3:42574800-42590200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:42575200-42589200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:42575200-42594400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:42575600-42590000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:42575800-42581000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr3:42575800-42581400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr3:42576200-42580800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:42576200-42581200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:42576600-42586000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:42577200-42581000	Weak transcription	Fetal Intestine Large	intestine
25	chr3:42577400-42581200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:42577400-42590800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:42577400-42592800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:42577600-42592000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:42577800-42597600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:42578000-42580800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:42578200-42581200	Weak transcription	Placenta	Placenta
32	chr3:42578400-42580800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr3:42578400-42581000	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr3:42578400-42581200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:42578400-42581200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr3:42578400-42586400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:42578400-42586800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:42578400-42593200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr3:42578400-42593400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr3:42578600-42580800	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr3:42578600-42581200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr3:42578600-42583800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr3:42578600-42586200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:42578800-42580800	Weak transcription	Lung	lung
45	chr3:42579200-42581000	Weak transcription	Spleen	Spleen
46	chr3:42579800-42582400	Weak transcription	Adipose Nuclei	Adipose
47	chr3:42580000-42581000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr3:42580000-42584000	Weak transcription	Esophagus	oesophagus
49	chr3:42580000-42589800	Weak transcription	Primary T cells from cord blood	blood
50	chr3:42580200-42581000	Weak transcription	Fetal Intestine Small	intestine

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