Variant report

Variant	rs13103035
Chromosome Location	chr4:78716152-78716153
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:78715797..78717361-chr9:125546307..125548582,2	MCF-7	breast:
2	chr4:78714906..78717368-chr4:78741847..78743752,2	K562	blood:
3	chr4:78714074..78716537-chr4:78722174..78724002,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10033527	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10033613	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11097938	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11728886	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11729215	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12645742	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13101418	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs13101987	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13103523	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13104947	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13106067	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs13119606	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13120272	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16996915	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2134050	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28404443	0.86[ASN][1000 genomes]
rs28855210	0.80[ASN][1000 genomes]
rs34830788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35735677	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4453957	0.91[ASN][1000 genomes]
rs4571357	0.81[ASN][1000 genomes]
rs4577601	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs4859509	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4859511	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4859875	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859877	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859879	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859888	0.85[ASN][1000 genomes]
rs4859889	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.83[ASN][1000 genomes]
rs6533282	0.85[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6533291	0.91[ASN][1000 genomes]
rs6533344	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs6814912	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs6848029	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6854895	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs7670157	0.82[ASW][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.96[MKK][hapmap];0.86[ASN][1000 genomes]
rs7675009	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7676660	0.84[ASN][1000 genomes]
rs7698627	0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829976	chr4:78576657-78757798	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv879501	chr4:78647634-78866007	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	esv1818157	chr4:78678104-78849088	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2752050	chr4:78693311-78975321	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13103035	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL
rs13103035	MRPL1	cis	parietal	SCAN
rs13103035	MRPL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78650200-78720000	Weak transcription	Spleen	Spleen
2	chr4:78694200-78722000	Weak transcription	Fetal Stomach	stomach
3	chr4:78696400-78717600	Weak transcription	Thymus	Thymus
4	chr4:78697200-78716400	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr4:78697400-78721400	Weak transcription	Placenta	Placenta
6	chr4:78698000-78716400	Weak transcription	Primary B cells from cord blood	blood
7	chr4:78698600-78717400	Weak transcription	Right Ventricle	heart
8	chr4:78698600-78720200	Weak transcription	Dnd41	blood
9	chr4:78698800-78717400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:78699200-78716400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:78701600-78716600	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr4:78701600-78721400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr4:78703600-78718000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr4:78704800-78716600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr4:78704800-78716600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr4:78704800-78722200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr4:78705800-78720000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr4:78706000-78717600	Weak transcription	Right Atrium	heart
19	chr4:78706200-78719800	Weak transcription	Fetal Intestine Small	intestine
20	chr4:78707000-78716600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr4:78707400-78720200	Weak transcription	Gastric	stomach
22	chr4:78707600-78717800	Weak transcription	Esophagus	oesophagus
23	chr4:78708000-78716400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr4:78709200-78721400	Weak transcription	Brain Substantia Nigra	brain
25	chr4:78710200-78722000	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr4:78710600-78716600	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr4:78711000-78717600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:78711000-78718000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr4:78711000-78722200	Weak transcription	Ovary	ovary
30	chr4:78711400-78716400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr4:78711400-78722000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr4:78711600-78721400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:78711600-78722200	Weak transcription	Brain Hippocampus Middle	brain
34	chr4:78711800-78721800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr4:78712000-78718000	Weak transcription	NHEK	skin
36	chr4:78712800-78722000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr4:78713200-78716200	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr4:78713600-78721600	Weak transcription	HUVEC	blood vessel
39	chr4:78714200-78720200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:78714200-78721200	Weak transcription	Colon Smooth Muscle	Colon
41	chr4:78714200-78721600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr4:78714600-78716800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr4:78714800-78716400	Weak transcription	Left Ventricle	heart
44	chr4:78714800-78716600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr4:78714800-78716600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr4:78714800-78716600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr4:78714800-78716600	Weak transcription	Lung	lung
48	chr4:78714800-78716600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr4:78714800-78717600	Weak transcription	Pancreas	Pancrea
50	chr4:78714800-78719000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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