Variant report

Variant	rs342507
Chromosome Location	chr3:42581680-42581681
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42288683..42289698-chr3:42581102..42582025,5	MCF-7	breast:
2	chr3:42288717..42289683-chr3:42581567..42582480,3	MCF-7	breast:
3	chr3:42580840..42582471-chr3:42621463..42624161,2	K562	blood:
4	chr3:42581119..42581953-chr3:42676306..42676872,2	K562	blood:
5	chr3:42271298..42272062-chr3:42581475..42581976,2	K562	blood:
6	chr3:42543347..42544924-chr3:42580025..42581850,2	K562	blood:

Variant related genes	Relation type
ENSG00000093183	Chromatin interaction
ENSG00000008324	Chromatin interaction
ENSG00000114857	Chromatin interaction
ENSG00000114812	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs2136012	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2271186	0.81[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs2976533	0.81[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs339658	0.81[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs339726	0.81[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs339727	0.81[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs342508	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	0.85[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs342522	0.84[ASN][1000 genomes]
rs342536	0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs342537	0.83[ASN][1000 genomes]
rs3774398	0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs4549	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs607568	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs639692	0.81[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs640689	0.81[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs6441892	0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs663673	0.81[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs689251	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs8351	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs925457	0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs342507	NKTR	cis	multi-tissue	Pritchard
rs342507	NKTR	cis	parietal	SCAN
rs342507	VIPR1	cis	cerebellum	SCAN
rs342507	NKTR	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42557800-42586000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr3:42557800-42590400	Weak transcription	Aorta	Aorta
3	chr3:42558000-42585200	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:42562400-42586800	Weak transcription	Small Intestine	intestine
5	chr3:42571800-42586200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:42574600-42585000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:42574800-42585600	Weak transcription	Brain Anterior Caudate	brain
8	chr3:42574800-42590200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:42575200-42589200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:42575200-42594400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:42575600-42590000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:42576600-42586000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:42577400-42590800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:42577400-42592800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:42577600-42592000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:42577800-42597600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:42578400-42586400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:42578400-42586800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:42578400-42593200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:42578400-42593400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:42578600-42583800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr3:42578600-42586200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:42579800-42582400	Weak transcription	Adipose Nuclei	Adipose
24	chr3:42580000-42584000	Weak transcription	Esophagus	oesophagus
25	chr3:42580000-42589800	Weak transcription	Primary T cells from cord blood	blood
26	chr3:42580600-42582000	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr3:42580600-42582200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:42580800-42582000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr3:42580800-42582200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:42580800-42582200	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr3:42580800-42582200	Enhancers	Primary T cells fromperipheralblood	blood
32	chr3:42580800-42582200	Enhancers	Duodenum Mucosa	Duodenum
33	chr3:42580800-42583000	Enhancers	Stomach Mucosa	stomach
34	chr3:42580800-42588600	Enhancers	Lung	lung
35	chr3:42581000-42582000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr3:42581000-42582200	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr3:42581000-42582600	Enhancers	Pancreas	Pancrea
38	chr3:42581000-42582600	Enhancers	Right Ventricle	heart
39	chr3:42581000-42582800	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr3:42581000-42582800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
41	chr3:42581000-42583000	Enhancers	Fetal Intestine Large	intestine
42	chr3:42581000-42583000	Enhancers	Fetal Intestine Small	intestine
43	chr3:42581000-42583000	Enhancers	Spleen	Spleen
44	chr3:42581000-42587000	Enhancers	Gastric	stomach
45	chr3:42581200-42581800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:42581200-42581800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:42581200-42581800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:42581200-42581800	Enhancers	Placenta	Placenta
49	chr3:42581200-42582000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:42581200-42582000	Enhancers	Rectal Mucosa Donor 29	rectum

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