Variant report

Variant	rs9496935
Chromosome Location	chr6:144657022-144657023
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF3	chr6:144657004-144657432	GM12878	blood:	n/a	chr6:144657315-144657325 chr6:144657310-144657323 chr6:144657313-144657327
2	FOS	chr6:144656994-144657304	MCF10A-Er-Src	breast:	n/a	chr6:144657180-144657189 chr6:144657178-144657190 chr6:144657179-144657188 chr6:144657180-144657187 chr6:144657179-144657189
3	FOS	chr6:144656995-144657337	MCF10A-Er-Src	breast:	n/a	chr6:144657180-144657189 chr6:144657178-144657190 chr6:144657179-144657188 chr6:144657180-144657187 chr6:144657179-144657189
4	FOS	chr6:144656996-144657344	MCF10A-Er-Src	breast:	n/a	chr6:144657180-144657189 chr6:144657178-144657190 chr6:144657179-144657188 chr6:144657180-144657187 chr6:144657179-144657189

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:144651729..144654747-chr6:144656256..144659237,4	MCF-7	breast:
2	chr6:144656543..144658129-chr6:144660023..144661876,2	K562	blood:

Variant related genes	Relation type
ENSG00000225311	TF binding region
ENSG00000225311	Chromatin interaction

Extended variants
information (count: 143 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs12660406	1.00[EUR][1000 genomes]
rs12660513	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs12660531	0.83[JPT][hapmap];1.00[EUR][1000 genomes]
rs12660596	1.00[EUR][1000 genomes]
rs12661781	1.00[EUR][1000 genomes]
rs12661969	0.84[CHB][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12662267	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12662696	1.00[EUR][1000 genomes]
rs12662724	1.00[EUR][1000 genomes]
rs12662786	1.00[EUR][1000 genomes]
rs12662872	1.00[EUR][1000 genomes]
rs12662904	1.00[EUR][1000 genomes]
rs12663172	1.00[EUR][1000 genomes]
rs12663380	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12663605	1.00[EUR][1000 genomes]
rs12663851	1.00[EUR][1000 genomes]
rs12664200	1.00[EUR][1000 genomes]
rs12664245	1.00[EUR][1000 genomes]
rs12664298	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs12664304	1.00[EUR][1000 genomes]
rs12665589	1.00[EUR][1000 genomes]
rs12665850	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17073442	1.00[EUR][1000 genomes]
rs17073463	1.00[EUR][1000 genomes]
rs17073482	1.00[EUR][1000 genomes]
rs17073498	1.00[EUR][1000 genomes]
rs17073506	1.00[EUR][1000 genomes]
rs17073524	1.00[EUR][1000 genomes]
rs17073528	1.00[EUR][1000 genomes]
rs17073529	1.00[EUR][1000 genomes]
rs17073544	1.00[EUR][1000 genomes]
rs17073571	1.00[EUR][1000 genomes]
rs17073580	1.00[EUR][1000 genomes]
rs17073598	1.00[EUR][1000 genomes]
rs17073602	1.00[EUR][1000 genomes]
rs17073610	1.00[EUR][1000 genomes]
rs17073623	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs17073629	1.00[EUR][1000 genomes]
rs17073631	1.00[EUR][1000 genomes]
rs17073672	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17073678	1.00[EUR][1000 genomes]
rs17840301	1.00[EUR][1000 genomes]
rs1998367	1.00[EUR][1000 genomes]
rs34140249	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34502493	1.00[EUR][1000 genomes]
rs35325795	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35681372	1.00[EUR][1000 genomes]
rs36007040	1.00[EUR][1000 genomes]
rs3811097	1.00[EUR][1000 genomes]
rs4301321	1.00[EUR][1000 genomes]
rs4896714	1.00[EUR][1000 genomes]
rs4896715	1.00[EUR][1000 genomes]
rs4896717	1.00[EUR][1000 genomes]
rs55684976	1.00[EUR][1000 genomes]
rs56820385	1.00[EUR][1000 genomes]
rs56897751	1.00[EUR][1000 genomes]
rs57069580	1.00[EUR][1000 genomes]
rs57380483	1.00[EUR][1000 genomes]
rs57485302	1.00[EUR][1000 genomes]
rs57592921	1.00[EUR][1000 genomes]
rs57679521	1.00[EUR][1000 genomes]
rs57704478	1.00[EUR][1000 genomes]
rs57712072	1.00[EUR][1000 genomes]
rs57751197	1.00[EUR][1000 genomes]
rs58084770	1.00[EUR][1000 genomes]
rs58396690	1.00[EUR][1000 genomes]
rs58590469	1.00[EUR][1000 genomes]
rs58646546	0.96[ASN][1000 genomes]
rs58847604	1.00[EUR][1000 genomes]
rs58849686	1.00[EUR][1000 genomes]
rs58857193	1.00[EUR][1000 genomes]
rs59003501	1.00[EUR][1000 genomes]
rs59612420	1.00[EUR][1000 genomes]
rs59614628	1.00[EUR][1000 genomes]
rs59718967	1.00[EUR][1000 genomes]
rs59803839	1.00[EUR][1000 genomes]
rs59810504	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59892317	0.84[ASN][1000 genomes]
rs59936141	1.00[EUR][1000 genomes]
rs60053855	1.00[EUR][1000 genomes]
rs60188478	1.00[EUR][1000 genomes]
rs60234245	1.00[EUR][1000 genomes]
rs60345197	1.00[EUR][1000 genomes]
rs60439721	1.00[EUR][1000 genomes]
rs60484357	1.00[EUR][1000 genomes]
rs60559108	1.00[EUR][1000 genomes]
rs60634096	1.00[EUR][1000 genomes]
rs60762289	1.00[EUR][1000 genomes]
rs60811448	1.00[EUR][1000 genomes]
rs60857439	1.00[EUR][1000 genomes]
rs60859726	1.00[EUR][1000 genomes]
rs61087655	1.00[EUR][1000 genomes]
rs61211447	1.00[EUR][1000 genomes]
rs61249035	1.00[EUR][1000 genomes]
rs61327932	1.00[EUR][1000 genomes]
rs6903993	0.80[AMR][1000 genomes]
rs6911171	0.96[AMR][1000 genomes]
rs6914753	1.00[EUR][1000 genomes]
rs6915621	1.00[EUR][1000 genomes]
rs6916795	1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs6917261	1.00[ASW][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6919115	0.96[AMR][1000 genomes]
rs6922109	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6922608	1.00[ASW][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6924797	0.84[AMR][1000 genomes]
rs6927798	1.00[ASW][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6941296	0.96[AMR][1000 genomes]
rs73588920	0.96[AMR][1000 genomes]
rs73589002	1.00[EUR][1000 genomes]
rs73591113	1.00[EUR][1000 genomes]
rs73594934	1.00[EUR][1000 genomes]
rs73594936	0.80[AMR][1000 genomes]
rs73594937	0.80[AMR][1000 genomes]
rs73780508	1.00[EUR][1000 genomes]
rs73780540	1.00[EUR][1000 genomes]
rs73780544	0.80[AMR][1000 genomes]
rs7741466	1.00[EUR][1000 genomes]
rs7743190	0.80[AMR][1000 genomes]
rs7745240	1.00[EUR][1000 genomes]
rs7745998	1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs7747486	1.00[EUR][1000 genomes]
rs7748278	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs7751351	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7751876	1.00[EUR][1000 genomes]
rs7754883	1.00[EUR][1000 genomes]
rs7761280	0.80[AMR][1000 genomes]
rs7766883	1.00[EUR][1000 genomes]
rs7768531	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs7774175	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9321968	1.00[MEX][hapmap];0.96[AMR][1000 genomes]
rs9321969	1.00[MEX][hapmap];0.96[AMR][1000 genomes]
rs9484874	1.00[EUR][1000 genomes]
rs9496925	0.96[AMR][1000 genomes]
rs9496928	0.96[AMR][1000 genomes]
rs9496930	0.84[AMR][1000 genomes]
rs9496932	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9496938	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9496944	0.84[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9496955	1.00[EUR][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	nsv830832	chr6:144572378-144759023	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2422260	chr6:144574591-144731630	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144639600-144660200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr6:144642200-144659800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:144643800-144663000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:144648200-144661200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:144648800-144672800	Weak transcription	Fetal Stomach	stomach
6	chr6:144649400-144660000	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:144651600-144659800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:144652000-144657200	Weak transcription	Fetal Intestine Large	intestine
9	chr6:144652000-144661000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr6:144652000-144668200	Weak transcription	Aorta	Aorta
11	chr6:144653000-144661200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:144653200-144657200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:144653200-144684600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:144653400-144657200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:144653400-144658000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:144653400-144658000	Weak transcription	Ovary	ovary
17	chr6:144653400-144658000	Weak transcription	NHDF-Ad	bronchial
18	chr6:144653400-144660000	Weak transcription	A549	lung
19	chr6:144653400-144661200	Weak transcription	Brain Anterior Caudate	brain
20	chr6:144653400-144662800	Weak transcription	Osteobl	bone
21	chr6:144653400-144665200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:144653600-144658000	Weak transcription	Fetal Lung	lung
23	chr6:144653600-144661400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:144653600-144662000	Weak transcription	NHLF	lung
25	chr6:144653600-144665000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:144654800-144658400	Enhancers	HSMMtube	muscle
27	chr6:144654800-144658800	Genic enhancers	HepG2	liver
28	chr6:144655200-144657200	Enhancers	H9 Cell Line	embryonic stem cell
29	chr6:144655200-144657200	Enhancers	Fetal Muscle Leg	muscle
30	chr6:144655200-144657600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:144655200-144657600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:144655200-144657600	Enhancers	NHEK	skin
33	chr6:144655200-144658000	Enhancers	Gastric	stomach
34	chr6:144655200-144658400	Enhancers	Left Ventricle	heart
35	chr6:144655400-144657400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:144655400-144657400	Enhancers	Right Atrium	heart
37	chr6:144655400-144662000	Weak transcription	HUVEC	blood vessel
38	chr6:144655600-144657200	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr6:144655600-144657200	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr6:144655600-144658200	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr6:144655600-144658200	Enhancers	Placenta	Placenta
42	chr6:144655600-144658400	Enhancers	Esophagus	oesophagus
43	chr6:144655600-144658400	Enhancers	Lung	lung
44	chr6:144655600-144658400	Enhancers	Pancreas	Pancrea
45	chr6:144655600-144658400	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr6:144655600-144658600	Enhancers	Stomach Mucosa	stomach
47	chr6:144655800-144657200	Enhancers	Brain Hippocampus Middle	brain
48	chr6:144655800-144657400	Enhancers	HSMM	muscle
49	chr6:144655800-144657600	Enhancers	Liver	Liver
50	chr6:144655800-144658400	Enhancers	Right Ventricle	heart

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