Variant report

Variant	rs16860720
Chromosome Location	chr3:112975021-112975022
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	chr3:112970765..112972828-chr3:112974570..112977015,2	MCF-7	breast:
2	chr3:112973746..112975579-chr3:112978657..112981572,2	K562	blood:

Variant related genes	Relation type
ENSG00000144857	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1499898	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16845106	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs16860709	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16860734	0.82[YRI][hapmap];0.91[AFR][1000 genomes]
rs16860770	0.82[ASN][1000 genomes]
rs17320040	1.00[ASN][1000 genomes]
rs17320242	1.00[ASN][1000 genomes]
rs2399476	0.82[ASN][1000 genomes]
rs28679287	0.91[AFR][1000 genomes]
rs34600669	0.82[ASN][1000 genomes]
rs3814399	0.88[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap]
rs3995908	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[AFR][1000 genomes]
rs41271353	0.82[ASN][1000 genomes]
rs57104308	0.93[ASN][1000 genomes]
rs59590258	0.82[ASN][1000 genomes]
rs60070011	1.00[ASN][1000 genomes]
rs61035513	1.00[ASN][1000 genomes]
rs9819129	0.91[AFR][1000 genomes]
rs9820139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9820627	0.82[YRI][hapmap];0.91[AFR][1000 genomes]
rs9823770	0.82[YRI][hapmap];0.91[AFR][1000 genomes]
rs9832953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9837357	0.91[AFR][1000 genomes]
rs9849714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853439	0.91[AFR][1000 genomes]
rs9855011	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864630	0.82[AFR][1000 genomes]
rs9869371	0.91[AFR][1000 genomes]
rs9872998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9878424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs998647	0.95[ASN][1000 genomes]
rs999365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1003511	chr3:112858775-112989045	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16860720	SNAR-A2	trans	lymphoblastoid	seeQTL
rs16860720	SNAR-A1	trans	lymphoblastoid	seeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112961600-112983000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:112968600-112980000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:112969000-112995200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr3:112969600-112981000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:112969800-112991800	Weak transcription	Right Ventricle	heart
6	chr3:112969800-112994200	Weak transcription	Spleen	Spleen
7	chr3:112970200-112981000	Weak transcription	Gastric	stomach
8	chr3:112970200-112981000	Weak transcription	Pancreas	Pancrea
9	chr3:112971200-112975400	Genic enhancers	Fetal Muscle Trunk	muscle
10	chr3:112971200-112978200	Genic enhancers	Fetal Muscle Leg	muscle
11	chr3:112971800-112986400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:112972000-112980600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:112972400-112986400	Weak transcription	Fetal Intestine Small	intestine
14	chr3:112972600-112975200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:112972600-112975600	Enhancers	HSMM	muscle
16	chr3:112972800-112976400	Enhancers	HSMMtube	muscle
17	chr3:112973200-112975200	Enhancers	GM12878-XiMat	blood
18	chr3:112973400-112976400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:112973400-112981800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:112973400-112982600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:112973400-112987600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:112973600-112977000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:112973600-112978600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:112973600-112978800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:112973600-112980400	Weak transcription	Brain Germinal Matrix	brain
26	chr3:112973600-112980400	Weak transcription	Fetal Kidney	kidney
27	chr3:112973600-112982000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr3:112973600-112983600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:112973600-112993000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:112973600-112997200	Weak transcription	Colonic Mucosa	Colon
31	chr3:112973800-112975200	Weak transcription	Left Ventricle	heart
32	chr3:112973800-112977800	Weak transcription	Adipose Nuclei	Adipose
33	chr3:112973800-112977800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:112973800-112978600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:112973800-112979400	Weak transcription	Aorta	Aorta
36	chr3:112973800-112979400	Weak transcription	Esophagus	oesophagus
37	chr3:112973800-112981200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:112973800-112981800	Weak transcription	Psoas Muscle	Psoas
39	chr3:112973800-112983400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
40	chr3:112974000-112975800	Strong transcription	Colon Smooth Muscle	Colon
41	chr3:112974000-112979400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:112974000-112979600	Weak transcription	Fetal Brain Female	brain
43	chr3:112974200-112975200	Weak transcription	Fetal Lung	lung
44	chr3:112974200-112976000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:112974200-112977000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:112974200-112977600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:112974200-112978000	Weak transcription	Ovary	ovary
48	chr3:112974200-112980200	Weak transcription	Fetal Brain Male	brain
49	chr3:112974200-112981000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:112974200-112981400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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