Variant report

Variant	rs9833500
Chromosome Location	chr3:46978549-46978550
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46967009..46980239-chr3:47015804..47024437,23	MCF-7	breast:
2	chr3:46975931..46978927-chr3:47032747..47034555,2	K562	blood:
3	chr3:46974856..46983636-chr3:47025231..47032249,9	K562	blood:
4	chr3:46969295..46972082-chr3:46977350..46978888,2	K562	blood:
5	chr3:46975584..46977390-chr3:46978479..46982012,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160796	Chromatin interaction
ENSG00000160799	Chromatin interaction

Extended variants
information (count: 145 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs10461017	1.00[EUR][1000 genomes]
rs10461019	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10865945	1.00[EUR][1000 genomes]
rs11130108	1.00[EUR][1000 genomes]
rs11130109	1.00[EUR][1000 genomes]
rs11706212	1.00[EUR][1000 genomes]
rs11708257	1.00[EUR][1000 genomes]
rs11709693	1.00[EUR][1000 genomes]
rs11709876	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11713537	1.00[EUR][1000 genomes]
rs11928558	1.00[EUR][1000 genomes]
rs12330516	1.00[EUR][1000 genomes]
rs12487763	1.00[EUR][1000 genomes]
rs13062185	1.00[EUR][1000 genomes]
rs13078181	1.00[EUR][1000 genomes]
rs13079416	1.00[EUR][1000 genomes]
rs13082531	1.00[EUR][1000 genomes]
rs13323092	1.00[EUR][1000 genomes]
rs1378818	1.00[EUR][1000 genomes]
rs1463394	1.00[EUR][1000 genomes]
rs1466272	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1466273	1.00[EUR][1000 genomes]
rs1473382	1.00[EUR][1000 genomes]
rs1473384	1.00[EUR][1000 genomes]
rs1473385	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1563431	1.00[EUR][1000 genomes]
rs1563432	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1814564	1.00[EUR][1000 genomes]
rs1869870	1.00[EUR][1000 genomes]
rs1979736	1.00[EUR][1000 genomes]
rs2124509	1.00[EUR][1000 genomes]
rs2350642	1.00[EUR][1000 genomes]
rs2385863	1.00[EUR][1000 genomes]
rs2385868	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs28735306	1.00[EUR][1000 genomes]
rs34147581	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35366910	1.00[EUR][1000 genomes]
rs4018904	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4282092	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4289375	1.00[EUR][1000 genomes]
rs4324490	1.00[EUR][1000 genomes]
rs4373094	1.00[EUR][1000 genomes]
rs4378998	1.00[EUR][1000 genomes]
rs4389512	1.00[EUR][1000 genomes]
rs4450857	1.00[EUR][1000 genomes]
rs4478107	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4522803	1.00[EUR][1000 genomes]
rs4525902	1.00[EUR][1000 genomes]
rs4543047	1.00[EUR][1000 genomes]
rs4682828	1.00[EUR][1000 genomes]
rs4682832	1.00[EUR][1000 genomes]
rs4682833	1.00[EUR][1000 genomes]
rs4682834	1.00[EUR][1000 genomes]
rs4682835	1.00[EUR][1000 genomes]
rs4682836	1.00[EUR][1000 genomes]
rs4682838	1.00[EUR][1000 genomes]
rs4682841	1.00[EUR][1000 genomes]
rs4682843	1.00[EUR][1000 genomes]
rs4682846	1.00[EUR][1000 genomes]
rs4682847	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4683277	1.00[EUR][1000 genomes]
rs4683279	1.00[EUR][1000 genomes]
rs4683282	1.00[TSI][hapmap]
rs4683283	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4683284	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4683285	1.00[EUR][1000 genomes]
rs4683286	1.00[EUR][1000 genomes]
rs4683288	1.00[EUR][1000 genomes]
rs4683289	1.00[EUR][1000 genomes]
rs4683290	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4683291	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4683292	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4683293	1.00[EUR][1000 genomes]
rs4683303	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6442041	1.00[EUR][1000 genomes]
rs6442042	1.00[EUR][1000 genomes]
rs6442043	1.00[EUR][1000 genomes]
rs6442044	1.00[EUR][1000 genomes]
rs6442047	1.00[EUR][1000 genomes]
rs6442048	1.00[EUR][1000 genomes]
rs6442062	1.00[EUR][1000 genomes]
rs6442063	1.00[EUR][1000 genomes]
rs6766676	1.00[EUR][1000 genomes]
rs6768169	1.00[EUR][1000 genomes]
rs6775797	1.00[EUR][1000 genomes]
rs6780994	1.00[EUR][1000 genomes]
rs6785462	1.00[EUR][1000 genomes]
rs6804732	1.00[EUR][1000 genomes]
rs6806521	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6808052	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6808629	1.00[EUR][1000 genomes]
rs6809904	1.00[EUR][1000 genomes]
rs73831482	1.00[EUR][1000 genomes]
rs7615774	1.00[EUR][1000 genomes]
rs7621530	1.00[EUR][1000 genomes]
rs7624549	1.00[EUR][1000 genomes]
rs7630154	1.00[EUR][1000 genomes]
rs7630904	1.00[EUR][1000 genomes]
rs7638549	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7641494	1.00[EUR][1000 genomes]
rs7643868	1.00[EUR][1000 genomes]
rs7644382	1.00[EUR][1000 genomes]
rs7646076	1.00[EUR][1000 genomes]
rs7649941	1.00[EUR][1000 genomes]
rs7650142	1.00[EUR][1000 genomes]
rs7652492	1.00[EUR][1000 genomes]
rs936173	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs936177	1.00[EUR][1000 genomes]
rs936178	1.00[EUR][1000 genomes]
rs936179	1.00[EUR][1000 genomes]
rs936180	1.00[EUR][1000 genomes]
rs936181	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs936182	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs936185	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs936186	1.00[EUR][1000 genomes]
rs9810881	1.00[EUR][1000 genomes]
rs9812407	1.00[EUR][1000 genomes]
rs9819344	1.00[EUR][1000 genomes]
rs9819475	1.00[EUR][1000 genomes]
rs9823480	1.00[EUR][1000 genomes]
rs9826488	1.00[EUR][1000 genomes]
rs9827293	1.00[EUR][1000 genomes]
rs9828473	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9836801	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9850151	1.00[EUR][1000 genomes]
rs9852167	1.00[EUR][1000 genomes]
rs9861247	1.00[EUR][1000 genomes]
rs9861265	1.00[EUR][1000 genomes]
rs9862711	1.00[EUR][1000 genomes]
rs9869489	1.00[EUR][1000 genomes]
rs9878813	1.00[EUR][1000 genomes]
rs9883152	1.00[EUR][1000 genomes]
rs9883909	1.00[EUR][1000 genomes]
rs9990284	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv460526	chr3:46935527-47001350	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv3800	chr3:46961648-47007241	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1012682	chr3:46973552-47016357	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46967400-46984400	Genic enhancers	Fetal Intestine Small	intestine
2	chr3:46968000-46978800	Enhancers	Stomach Mucosa	stomach
3	chr3:46970200-46978600	Enhancers	Right Ventricle	heart
4	chr3:46970800-46979400	Enhancers	HUVEC	blood vessel
5	chr3:46970800-46984200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:46971200-46988400	Strong transcription	Dnd41	blood
7	chr3:46971600-46978600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr3:46971800-46980000	Enhancers	Psoas Muscle	Psoas
9	chr3:46971800-46982800	Enhancers	Right Atrium	heart
10	chr3:46972400-46978800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr3:46972400-46981200	Genic enhancers	Fetal Muscle Leg	muscle
12	chr3:46973800-46982400	Genic enhancers	Primary B cells from peripheral blood	blood
13	chr3:46973800-46985600	Weak transcription	Fetal Kidney	kidney
14	chr3:46974000-46988600	Strong transcription	Primary T cells from cord blood	blood
15	chr3:46974200-46979200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr3:46974800-46978800	Genic enhancers	K562	blood
17	chr3:46975000-46979400	Genic enhancers	NHLF	lung
18	chr3:46975000-46986000	Strong transcription	Thymus	Thymus
19	chr3:46975600-46979000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:46975600-46979200	Enhancers	NH-A	brain
21	chr3:46975600-46982800	Genic enhancers	Fetal Intestine Large	intestine
22	chr3:46975800-46978600	Enhancers	Placenta Amnion	Placenta Amnion
23	chr3:46975800-46978800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr3:46975800-46984800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr3:46976000-46979200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:46976000-46985600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:46976200-46980400	Genic enhancers	Fetal Muscle Trunk	muscle
28	chr3:46976200-46980600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:46976200-46982400	Genic enhancers	Spleen	Spleen
30	chr3:46976200-46983200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr3:46976200-46990200	Weak transcription	Fetal Brain Male	brain
32	chr3:46976400-46978600	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr3:46976400-46978600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:46976400-46979000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:46976400-46979600	Strong transcription	GM12878-XiMat	blood
36	chr3:46976600-46978800	Enhancers	HSMMtube	muscle
37	chr3:46976800-46979600	Strong transcription	Fetal Thymus	thymus
38	chr3:46977000-46978600	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr3:46977000-46978600	Genic enhancers	NHEK	skin
40	chr3:46977000-46978800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr3:46977000-46978800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:46977000-46978800	Enhancers	Brain Hippocampus Middle	brain
43	chr3:46977000-46979000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:46977000-46980600	Weak transcription	Aorta	Aorta
45	chr3:46977000-46982800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:46977000-47000000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:46977200-46979600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:46977200-46981600	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:46977200-46982800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:46977400-46978600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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