Variant report

Variant	rs9754657
Chromosome Location	chr3:17771230-17771231
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	chr3:17769377..17773406-chr3:17782052..17786332,6	MCF-7	breast:
2	chr3:17753447..17755867-chr3:17768975..17771432,2	K562	blood:

Variant related genes	Relation type
ENSG00000131374	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs11914537	0.86[YRI][hapmap];0.87[AMR][1000 genomes]
rs11914797	0.92[YRI][hapmap];0.87[AMR][1000 genomes]
rs11915560	0.88[YRI][hapmap];0.87[AMR][1000 genomes]
rs11916424	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11921699	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11922861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11923635	0.88[YRI][hapmap];0.87[AMR][1000 genomes]
rs11924147	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11924560	1.00[EUR][1000 genomes]
rs11925066	0.81[YRI][hapmap]
rs11925226	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11925353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11926072	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11926087	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11926251	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11927232	1.00[EUR][1000 genomes]
rs11927283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11927769	0.88[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11927967	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11929046	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11929521	1.00[EUR][1000 genomes]
rs12106899	0.88[YRI][hapmap];0.87[AMR][1000 genomes]
rs12106900	0.87[AMR][1000 genomes]
rs12107061	1.00[EUR][1000 genomes]
rs12152509	0.87[AMR][1000 genomes]
rs12185952	0.87[AMR][1000 genomes]
rs28525383	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57352109	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58152540	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58392667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58848058	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58921548	1.00[EUR][1000 genomes]
rs59582994	0.87[AMR][1000 genomes]
rs59891221	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59960076	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60245392	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60459720	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60662240	1.00[EUR][1000 genomes]
rs60803166	1.00[EUR][1000 genomes]
rs60838916	1.00[EUR][1000 genomes]
rs60940413	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs61650046	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61698855	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6577595	1.00[EUR][1000 genomes]
rs6577629	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6763348	1.00[EUR][1000 genomes]
rs6796915	1.00[EUR][1000 genomes]
rs73160940	0.87[AMR][1000 genomes]
rs73160942	0.87[AMR][1000 genomes]
rs73160943	0.87[AMR][1000 genomes]
rs73160950	0.87[AMR][1000 genomes]
rs73160951	0.87[AMR][1000 genomes]
rs73160957	0.87[AMR][1000 genomes]
rs73160959	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73160964	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73160967	0.87[AMR][1000 genomes]
rs73164768	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73164787	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73164796	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165722	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165729	0.87[AMR][1000 genomes]
rs73165734	0.87[AMR][1000 genomes]
rs73165735	0.87[AMR][1000 genomes]
rs73165736	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165740	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165743	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165752	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165764	0.87[AMR][1000 genomes]
rs73165771	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165774	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165775	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165777	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165779	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165792	0.87[AMR][1000 genomes]
rs73165798	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73166516	1.00[EUR][1000 genomes]
rs73166544	1.00[EUR][1000 genomes]
rs73167503	1.00[AMR][1000 genomes]
rs73167510	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73167513	1.00[EUR][1000 genomes]
rs73167514	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73167523	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73167527	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73168748	1.00[EUR][1000 genomes]
rs73168752	1.00[EUR][1000 genomes]
rs73170844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73170855	1.00[EUR][1000 genomes]
rs73170858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73170877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73170878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73172909	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73172914	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73172924	1.00[EUR][1000 genomes]
rs7619879	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7620585	0.88[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7630381	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7631803	1.00[EUR][1000 genomes]
rs7648122	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9680896	1.00[EUR][1000 genomes]
rs9754654	0.93[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9941993	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9968236	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013069	chr3:17560456-17783372	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv999594	chr3:17690416-17982318	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17755200-17771800	Weak transcription	Brain Angular Gyrus	brain
2	chr3:17755400-17781600	Weak transcription	Pancreas	Pancrea
3	chr3:17756200-17774600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:17756200-17782400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:17756400-17780600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:17756400-17782800	Weak transcription	Aorta	Aorta
7	chr3:17756600-17771800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:17756600-17782200	Weak transcription	HSMM	muscle
9	chr3:17756800-17781600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:17756800-17782200	Weak transcription	NHLF	lung
11	chr3:17757000-17780600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:17757200-17771600	Weak transcription	HUVEC	blood vessel
13	chr3:17757200-17774400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr3:17757200-17780400	Weak transcription	Adipose Nuclei	Adipose
15	chr3:17757200-17780800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:17757200-17782200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:17757400-17771800	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:17757400-17780400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:17757400-17780600	Weak transcription	Small Intestine	intestine
20	chr3:17757400-17781600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:17757400-17782400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr3:17757600-17780600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:17757600-17781000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:17757600-17781600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:17757600-17782200	Weak transcription	Spleen	Spleen
26	chr3:17757600-17782400	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr3:17757600-17783200	Weak transcription	Ovary	ovary
28	chr3:17757800-17780000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:17758000-17773000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:17759200-17782200	Weak transcription	HSMMtube	muscle
31	chr3:17759600-17780000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:17759800-17772000	Weak transcription	Fetal Heart	heart
33	chr3:17759800-17778800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:17759800-17781600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:17761800-17771800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr3:17762200-17783400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:17762600-17782400	Weak transcription	Psoas Muscle	Psoas
38	chr3:17764200-17780200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr3:17764800-17782200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:17765000-17777200	Weak transcription	Lung	lung
41	chr3:17765000-17782200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr3:17765800-17781600	Weak transcription	HepG2	liver
43	chr3:17765800-17783400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:17766400-17782200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr3:17766800-17772200	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr3:17767000-17774600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:17767200-17771800	Weak transcription	Fetal Intestine Small	intestine
48	chr3:17767400-17771800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr3:17767600-17780600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr3:17767600-17781000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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