Variant report

Variant	rs9654194
Chromosome Location	chr4:78728697-78728698
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:78706089..78707597-chr4:78727049..78729369,2	K562	blood:
2	chr4:78727559..78729935-chr4:78732783..78735387,2	MCF-7	breast:
3	chr4:78725207..78728407-chr4:78728574..78730602,3	K562	blood:
4	chr4:78727738..78737799-chr4:78737984..78742271,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138767	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10005531	0.90[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.81[ASN][1000 genomes]
rs10005935	1.00[ASW][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10007837	0.82[YRI][hapmap]
rs10018117	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10019920	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs10026176	0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10027634	0.84[ASN][1000 genomes]
rs10030568	0.82[CHD][hapmap]
rs10049674	0.82[CHD][hapmap]
rs10222901	0.80[LWK][hapmap];0.83[YRI][hapmap]
rs11737861	0.80[LWK][hapmap]
rs11931686	0.94[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11942975	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12509847	0.88[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12510593	0.86[YRI][hapmap]
rs13131331	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1587563	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17002804	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1809919	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1996740	0.87[GIH][hapmap];0.84[MEX][hapmap]
rs2102116	0.80[LWK][hapmap];0.83[YRI][hapmap]
rs2134048	0.80[LWK][hapmap]
rs2173869	0.82[YRI][hapmap]
rs28436599	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2866688	0.83[YRI][hapmap]
rs2866690	0.82[YRI][hapmap]
rs28685099	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3205281	0.80[LWK][hapmap]
rs4128860	0.84[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.80[ASN][1000 genomes]
rs4304001	0.80[LWK][hapmap];0.83[YRI][hapmap]
rs4328941	0.84[ASN][1000 genomes]
rs4388114	0.83[YRI][hapmap]
rs4410552	0.80[LWK][hapmap];0.89[YRI][hapmap]
rs4859512	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs4859513	0.90[CHB][hapmap]
rs4859882	0.95[CHB][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4859884	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs4859890	0.84[CHB][hapmap];0.80[ASN][1000 genomes]
rs6533225	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6533372	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs67814821	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6811439	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6816134	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6825492	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6835993	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6839504	0.83[YRI][hapmap]
rs6849145	0.84[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.84[ASN][1000 genomes]
rs6850111	0.82[YRI][hapmap]
rs7436080	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs7660788	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7682450	0.90[CHB][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7687812	0.83[YRI][hapmap]
rs7698009	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs924684	0.90[CHB][hapmap];0.81[LWK][hapmap]
rs9994366	0.83[AMR][1000 genomes];0.83[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
rs9654194	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL
rs9654194	BTC	cis	parietal	SCAN
rs9654194	G3BP2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78716400-78733400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:78718800-78738600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr4:78720600-78732000	Weak transcription	Aorta	Aorta
4	chr4:78720800-78735600	Weak transcription	HepG2	liver
5	chr4:78721000-78732400	Weak transcription	Fetal Intestine Small	intestine
6	chr4:78722200-78738600	Weak transcription	HSMM	muscle
7	chr4:78722400-78734800	Weak transcription	Fetal Intestine Large	intestine
8	chr4:78722600-78729000	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr4:78722600-78732000	Weak transcription	Thymus	Thymus
10	chr4:78722600-78735800	Weak transcription	A549	lung
11	chr4:78722600-78737800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:78722600-78737800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr4:78722600-78738600	Weak transcription	NHEK	skin
14	chr4:78722600-78739000	Weak transcription	Ovary	ovary
15	chr4:78722600-78739200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr4:78722800-78732000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr4:78722800-78736800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:78722800-78738600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:78723000-78732000	Weak transcription	Right Atrium	heart
20	chr4:78723000-78732400	Weak transcription	Fetal Thymus	thymus
21	chr4:78723000-78732600	Enhancers	Primary T cells from cord blood	blood
22	chr4:78723000-78734800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:78723000-78738600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:78723200-78738600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr4:78724000-78732000	Weak transcription	Dnd41	blood
26	chr4:78724000-78735000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:78724000-78736000	Weak transcription	HUVEC	blood vessel
28	chr4:78724000-78736800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr4:78724200-78733600	Weak transcription	Primary B cells from cord blood	blood
30	chr4:78724400-78735600	Weak transcription	Liver	Liver
31	chr4:78724400-78738600	Weak transcription	Colonic Mucosa	Colon
32	chr4:78724800-78732800	Weak transcription	Duodenum Mucosa	Duodenum
33	chr4:78724800-78738600	Weak transcription	Brain Substantia Nigra	brain
34	chr4:78725000-78732800	Weak transcription	Small Intestine	intestine
35	chr4:78725600-78731800	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr4:78725600-78734800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr4:78725800-78736800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr4:78725800-78738600	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr4:78726000-78728800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr4:78727200-78731800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr4:78727200-78737800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr4:78727400-78732600	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr4:78727400-78733000	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr4:78727400-78735600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr4:78727400-78735800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr4:78727400-78735800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr4:78727600-78729600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr4:78727800-78728800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr4:78727800-78728800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr4:78727800-78732800	Strong transcription	Primary B cells from peripheral blood	blood

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