Variant report

Variant	rs9878078
Chromosome Location	chr3:136237573-136237574
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136237342..136239151-chr3:136470510..136472888,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118007	Chromatin interaction
ENSG00000261758	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs12695649	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062352	1.00[ASN][1000 genomes]
rs13066401	1.00[ASN][1000 genomes]
rs13071220	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13092193	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096466	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13100192	1.00[ASN][1000 genomes]
rs13316214	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13321721	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13326151	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13433688	0.93[CEU][hapmap];1.00[ASN][1000 genomes]
rs13434116	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1604793	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17200216	1.00[CEU][hapmap]
rs17298525	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17364492	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28390205	1.00[ASN][1000 genomes]
rs28472992	1.00[ASN][1000 genomes]
rs28634226	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs28641809	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28718456	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28750366	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28811905	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28877020	1.00[ASN][1000 genomes]
rs34031772	1.00[ASN][1000 genomes]
rs34135127	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34168675	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34282798	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34428695	1.00[ASN][1000 genomes]
rs34757183	0.84[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34804893	1.00[ASW][hapmap];0.93[CEU][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34913797	1.00[CEU][hapmap];0.82[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];1.00[ASN][1000 genomes]
rs34969907	1.00[ASN][1000 genomes]
rs35100027	1.00[ASN][1000 genomes]
rs35326900	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35428413	1.00[ASN][1000 genomes]
rs35522825	1.00[ASN][1000 genomes]
rs35899944	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4038586	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66890203	1.00[ASN][1000 genomes]
rs67145204	1.00[ASN][1000 genomes]
rs67382287	1.00[ASN][1000 genomes]
rs6767889	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768743	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771002	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773949	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774964	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775314	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67949818	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806123	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71336069	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230043	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7612425	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809269	1.00[ASN][1000 genomes]
rs9810789	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812579	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[ASN][1000 genomes]
rs9813115	1.00[ASN][1000 genomes]
rs9813376	1.00[ASN][1000 genomes]
rs9813691	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818056	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818536	1.00[ASN][1000 genomes]
rs9820717	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs9823373	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828088	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9832813	0.92[MEX][hapmap]
rs9837158	0.86[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs9838884	1.00[ASN][1000 genomes]
rs9839137	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9841529	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs9845862	1.00[ASN][1000 genomes]
rs9847427	0.93[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs9857833	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857966	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9866840	1.00[ASN][1000 genomes]
rs9869630	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870825	1.00[ASN][1000 genomes]
rs9873536	1.00[ASN][1000 genomes]
rs9875770	1.00[ASN][1000 genomes]
rs9880211	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9881831	1.00[ASN][1000 genomes]
rs9883189	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv877520	chr3:136056861-136310985	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv877521	chr3:136069286-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv877522	chr3:136088038-136241028	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv877523	chr3:136088038-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv520012	chr3:136088038-136314119	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv877524	chr3:136112109-136295283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv877525	chr3:136112109-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv877526	chr3:136149139-136310985	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv877527	chr3:136182053-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv877528	chr3:136209550-136295283	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv591850	chr3:136209550-136300732	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9878078	GRK7	cis	cerebellum	SCAN
rs9878078	PPP2R3A	cis	parietal	SCAN
rs9878078	PPP2R3A	cis	cerebellum	SCAN
rs9878078	ERICH1	trans	parietal	SCAN
rs9878078	NCK1	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136176400-136314200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:136176600-136240000	Weak transcription	HMEC	breast
3	chr3:136176600-136260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:136176800-136266200	Weak transcription	Hela-S3	cervix
5	chr3:136191400-136268000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:136192400-136252400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:136193800-136239200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:136195400-136241800	Weak transcription	NH-A	brain
9	chr3:136195400-136250400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:136195400-136278800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:136212200-136323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:136212400-136241600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:136212400-136249600	Weak transcription	Lung	lung
14	chr3:136212600-136248200	Weak transcription	Esophagus	oesophagus
15	chr3:136213000-136239000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:136213000-136251000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:136213000-136252200	Weak transcription	Left Ventricle	heart
18	chr3:136213000-136326600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:136213200-136246000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:136213200-136246600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:136214000-136239600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:136214000-136246200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:136214400-136238400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:136215600-136246200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:136220600-136240000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:136220600-136242800	Weak transcription	GM12878-XiMat	blood
27	chr3:136220600-136266200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:136221000-136246400	Weak transcription	Fetal Muscle Leg	muscle
29	chr3:136221200-136241200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:136221200-136251000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:136221400-136246400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr3:136221400-136251000	Weak transcription	Liver	Liver
33	chr3:136221600-136246200	Weak transcription	Fetal Intestine Large	intestine
34	chr3:136221600-136251000	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr3:136222000-136246200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:136222000-136246600	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr3:136222200-136238600	Weak transcription	Placenta	Placenta
38	chr3:136222200-136251000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:136222200-136251200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr3:136222400-136266200	Weak transcription	HSMM	muscle
41	chr3:136227800-136246600	Weak transcription	Fetal Thymus	thymus
42	chr3:136227800-136246600	Weak transcription	Thymus	Thymus
43	chr3:136230000-136246400	Weak transcription	Fetal Stomach	stomach
44	chr3:136230400-136251000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr3:136230600-136247600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr3:136230800-136246200	Weak transcription	Fetal Lung	lung
47	chr3:136232000-136241800	Weak transcription	Osteobl	bone
48	chr3:136232000-136263600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:136232200-136238200	Weak transcription	Psoas Muscle	Psoas
50	chr3:136232200-136246600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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