Variant report

Variant	rs11714216
Chromosome Location	chr3:120421373-120421374
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120421115..120423893-chr3:120461818..120463428,2	K562	blood:

Variant related genes	Relation type
ENSG00000144840	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11708525	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712360	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11713594	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716584	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11718363	0.89[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11719207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11719896	0.83[ASN][1000 genomes]
rs11720353	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720614	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17140281	1.00[YRI][hapmap]
rs17183618	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs17184204	0.84[ASN][1000 genomes]
rs17243218	0.89[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17243933	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2059331	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2229308	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2292170	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[ASN][1000 genomes]
rs2877413	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs34319994	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34565470	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41365345	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs55663109	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55869122	0.80[ASN][1000 genomes]
rs56140323	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56267829	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6438590	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769985	0.81[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs6779005	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73183728	0.83[ASN][1000 genomes]
rs73183730	0.80[ASN][1000 genomes]
rs7637037	0.87[ASN][1000 genomes]
rs7647895	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv877377	chr3:120287683-120426750	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv829699	chr3:120308332-120484695	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
8	nsv869548	chr3:120320731-121076337	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv916869	chr3:120360281-120973169	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv877378	chr3:120381530-120606438	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11714216	C3orf15	cis	lymphoblastoid	seeQTL
rs11714216	LOC100125556	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120397600-120421600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:120397800-120421800	Weak transcription	Aorta	Aorta
3	chr3:120397800-120424800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:120398200-120423200	Weak transcription	Psoas Muscle	Psoas
5	chr3:120398200-120427000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:120398200-120427800	Weak transcription	Placenta	Placenta
7	chr3:120398200-120430200	Weak transcription	NHEK	skin
8	chr3:120398200-120438000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:120398800-120442200	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:120400200-120421600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:120401000-120424800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:120402400-120423600	Weak transcription	Lung	lung
13	chr3:120402800-120421800	Weak transcription	Fetal Kidney	kidney
14	chr3:120402800-120456600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:120403600-120423800	Weak transcription	Spleen	Spleen
16	chr3:120404000-120423600	Weak transcription	Pancreas	Pancrea
17	chr3:120404800-120421800	Weak transcription	HSMM	muscle
18	chr3:120405600-120436800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:120406000-120421800	Weak transcription	Dnd41	blood
20	chr3:120406400-120436600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr3:120406600-120421800	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:120407000-120421800	Weak transcription	Thymus	Thymus
23	chr3:120407200-120422000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr3:120408400-120421800	Weak transcription	Fetal Thymus	thymus
25	chr3:120408400-120429400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:120408600-120427400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:120408800-120421600	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr3:120411000-120422800	Weak transcription	Fetal Lung	lung
29	chr3:120411000-120436600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:120412600-120421600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:120412600-120421800	Weak transcription	Adipose Nuclei	Adipose
32	chr3:120412600-120424400	Weak transcription	HMEC	breast
33	chr3:120412600-120425400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:120412800-120421600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:120412800-120422600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:120412800-120425200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:120412800-120425600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:120412800-120426600	Weak transcription	Brain Angular Gyrus	brain
39	chr3:120412800-120435600	Weak transcription	NH-A	brain
40	chr3:120412800-120438000	Weak transcription	Fetal Intestine Small	intestine
41	chr3:120413200-120421800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:120413200-120421800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:120413800-120423400	Weak transcription	Colonic Mucosa	Colon
44	chr3:120414400-120425000	Weak transcription	Brain Germinal Matrix	brain
45	chr3:120415000-120438000	Weak transcription	HepG2	liver
46	chr3:120415400-120425800	Weak transcription	A549	lung
47	chr3:120416000-120421600	Weak transcription	Esophagus	oesophagus
48	chr3:120416400-120423200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr3:120416400-120436800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr3:120416400-120437200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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