Variant report

Variant	rs55804512
Chromosome Location	chr3:43330621-43330622
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:43320796..43322949-chr3:43328990..43330664,2	K562	blood:
2	chr3:43327640..43330625-chr3:43731199..43733951,3	K562	blood:
3	chr3:43328459..43331117-chr3:43356191..43358697,2	K562	blood:
4	chr3:43329569..43331859-chr3:43336954..43339880,3	MCF-7	breast:
5	chr3:43327921..43329533-chr3:43329941..43331733,2	MCF-7	breast:
6	chr3:43325116..43327718-chr3:43329418..43331490,2	K562	blood:

Variant related genes	Relation type
ENSG00000160746	Chromatin interaction
ENSG00000163788	Chromatin interaction
ENSG00000011198	Chromatin interaction
ENSG00000241939	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs17075422	1.00[AMR][1000 genomes]
rs17075424	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075519	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075525	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075540	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075564	0.97[AFR][1000 genomes]
rs17075568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075581	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075614	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075617	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075623	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075624	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075696	0.85[AFR][1000 genomes]
rs17075709	0.90[AFR][1000 genomes]
rs17075750	0.85[AFR][1000 genomes]
rs17254716	1.00[AMR][1000 genomes]
rs17320381	1.00[AMR][1000 genomes]
rs17405728	1.00[AMR][1000 genomes]
rs17406148	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17406718	0.97[AFR][1000 genomes]
rs17472888	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2036617	1.00[AFR][1000 genomes]
rs2086652	0.90[AFR][1000 genomes]
rs34343482	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34730190	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41321344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4368477	0.90[AFR][1000 genomes]
rs55694436	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55727302	1.00[AMR][1000 genomes]
rs55730605	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55760455	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55765643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55786717	0.85[AFR][1000 genomes]
rs55837468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55864645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55887904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55908419	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55915337	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55919732	0.85[AFR][1000 genomes]
rs55951861	1.00[AMR][1000 genomes]
rs55957435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56100043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56209592	0.90[AFR][1000 genomes]
rs56225070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56282728	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56285372	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56286131	1.00[AMR][1000 genomes]
rs56388016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56395291	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56659864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56741341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56849726	0.90[AFR][1000 genomes]
rs57019763	1.00[AMR][1000 genomes]
rs57020473	1.00[AMR][1000 genomes]
rs57147822	0.85[AFR][1000 genomes]
rs57376786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58066802	0.90[AFR][1000 genomes]
rs58158782	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58209397	1.00[AMR][1000 genomes]
rs58216554	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58508138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58636339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58866653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59113361	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59121457	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59276993	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59433561	0.90[AFR][1000 genomes]
rs59495244	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59545985	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59706458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59872395	1.00[AMR][1000 genomes]
rs59930267	1.00[AMR][1000 genomes]
rs60689590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61270592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61375879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61644103	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73829182	1.00[AMR][1000 genomes]
rs73829183	1.00[AMR][1000 genomes]
rs73829189	1.00[AMR][1000 genomes]
rs73829191	1.00[AMR][1000 genomes]
rs73831214	1.00[AMR][1000 genomes]
rs73831218	1.00[AMR][1000 genomes]
rs73831224	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831226	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831227	1.00[AMR][1000 genomes]
rs73831230	0.94[AFR][1000 genomes]
rs73831232	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831242	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831256	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831267	1.00[AFR][1000 genomes]
rs73831271	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831273	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831274	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831275	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831277	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831279	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831280	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831281	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831283	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831285	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831287	0.87[AFR][1000 genomes]
rs73831288	0.90[AFR][1000 genomes]
rs73831291	0.90[AFR][1000 genomes]
rs73831292	0.90[AFR][1000 genomes]
rs73831294	0.90[AFR][1000 genomes]
rs73831295	0.90[AFR][1000 genomes]
rs73831296	0.90[AFR][1000 genomes]
rs73831297	0.90[AFR][1000 genomes]
rs73831301	0.90[AFR][1000 genomes]
rs73832606	0.90[AFR][1000 genomes]
rs73832607	0.85[AFR][1000 genomes]
rs984347	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752008	chr3:43285369-43360879	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1009102	chr3:43285369-43369712	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv876732	chr3:43326887-43360879	Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv590154	chr3:43327873-43334020	Enhancers Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv590155	chr3:43327873-43334878	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv590158	chr3:43327924-43334878	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv590160	chr3:43328076-43334878	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43327400-43332000	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr3:43327800-43330800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:43327800-43331200	Active TSS	Fetal Muscle Trunk	muscle
4	chr3:43328600-43330800	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr3:43328600-43331400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:43328800-43330800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
7	chr3:43328800-43331600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr3:43328800-43333000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr3:43329000-43331000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:43329000-43331400	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr3:43329200-43330800	Active TSS	HSMMtube	muscle
12	chr3:43329200-43331800	Flanking Active TSS	Liver	Liver
13	chr3:43329200-43333600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr3:43329200-43344800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:43329200-43346800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:43329400-43330800	Active TSS	Brain Cingulate Gyrus	brain
17	chr3:43329400-43330800	Enhancers	Fetal Heart	heart
18	chr3:43329400-43331400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr3:43329400-43331400	Enhancers	HSMM	muscle
20	chr3:43329400-43346400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:43329600-43331400	Enhancers	Fetal Brain Female	brain
22	chr3:43329600-43345000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:43329800-43331400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:43329800-43335000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:43330000-43330800	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr3:43330000-43330800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr3:43330000-43331200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:43330200-43330800	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr3:43330200-43330800	Flanking Active TSS	Fetal Intestine Large	intestine
30	chr3:43330200-43330800	Flanking Active TSS	Fetal Intestine Small	intestine
31	chr3:43330200-43330800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
32	chr3:43330200-43330800	Flanking Active TSS	Hela-S3	cervix
33	chr3:43330200-43331000	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr3:43330200-43331000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:43330200-43331000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
36	chr3:43330200-43331000	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:43330200-43331000	Flanking Active TSS	NHEK	skin
38	chr3:43330200-43331200	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr3:43330200-43331400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:43330200-43331400	Flanking Active TSS	Colon Smooth Muscle	Colon
41	chr3:43330200-43331400	Flanking Active TSS	Rectal Smooth Muscle	rectum
42	chr3:43330200-43331400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr3:43330200-43331600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr3:43330200-43332000	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr3:43330200-43332000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr3:43330200-43333000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:43330200-43333000	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr3:43330200-43333200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:43330200-43333400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:43330400-43330800	Enhancers	HUES64 Cell Line	embryonic stem cell

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