Variant report

Variant	rs55728374
Chromosome Location	chr1:161020997-161020998
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160989179..160991784-chr1:161020756..161022798,2	K562	blood:
2	chr1:160965107..160967123-chr1:161018782..161021042,2	MCF-7	breast:
3	chr1:161019790..161021495-chr1:161129242..161131145,2	MCF-7	breast:
4	chr1:160991163..160993549-chr1:161020053..161022442,2	MCF-7	breast:
5	chr1:161020801..161022470-chr1:161048503..161051319,2	K562	blood:
6	chr1:161018354..161021283-chr1:161024769..161026655,3	K562	blood:

Variant related genes	Relation type
ENSG00000158769	Chromatin interaction
ENSG00000143258	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1044478	0.82[AMR][1000 genomes]
rs1062826	0.83[AMR][1000 genomes]
rs1062827	0.83[AMR][1000 genomes]
rs11265542	0.89[EUR][1000 genomes]
rs11799478	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11799521	0.89[EUR][1000 genomes]
rs11807930	0.85[AMR][1000 genomes]
rs12401336	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12565932	0.83[AMR][1000 genomes]
rs17384360	0.87[AFR][1000 genomes]
rs17388108	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1806774	0.81[AMR][1000 genomes]
rs2073655	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2073656	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2073658	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2251597	0.85[EUR][1000 genomes]
rs2251728	0.85[EUR][1000 genomes]
rs2297219	0.83[AMR][1000 genomes]
rs2297220	0.83[AMR][1000 genomes]
rs2297221	0.83[AMR][1000 genomes]
rs2297222	0.83[AMR][1000 genomes]
rs2481084	0.85[EUR][1000 genomes]
rs2481085	0.90[EUR][1000 genomes]
rs3119321	0.89[EUR][1000 genomes]
rs3737785	0.83[AMR][1000 genomes]
rs3737787	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41267947	0.83[AMR][1000 genomes]
rs41267949	0.83[AMR][1000 genomes]
rs41267951	0.83[AMR][1000 genomes]
rs41269993	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4339888	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61803664	0.83[AMR][1000 genomes]
rs61803671	0.89[EUR][1000 genomes]
rs61803672	0.89[EUR][1000 genomes]
rs72712854	0.81[AMR][1000 genomes]
rs836	0.82[AMR][1000 genomes]
rs869985	0.83[AMR][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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv3221	chr1:161008175-161052979	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55728374	F11R	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161016200-161022600	Weak transcription	Gastric	stomach
2	chr1:161016400-161022600	Weak transcription	Small Intestine	intestine
3	chr1:161016400-161037800	Weak transcription	Colonic Mucosa	Colon
4	chr1:161016600-161022200	Weak transcription	Brain Anterior Caudate	brain
5	chr1:161016600-161024200	Weak transcription	Right Ventricle	heart
6	chr1:161016600-161028000	Weak transcription	Brain Substantia Nigra	brain
7	chr1:161016800-161021800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:161016800-161029200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:161017000-161022000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:161017000-161024200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:161017000-161029400	Strong transcription	Primary T cells from cord blood	blood
12	chr1:161017000-161031600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:161017000-161032200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:161017200-161021200	Weak transcription	Stomach Mucosa	stomach
15	chr1:161017200-161022000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:161017200-161029200	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr1:161017200-161030000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:161017400-161022600	Weak transcription	K562	blood
19	chr1:161017400-161027400	Strong transcription	Primary hematopoietic stem cells	blood
20	chr1:161017400-161027400	Strong transcription	Dnd41	blood
21	chr1:161017400-161030000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:161017400-161031000	Strong transcription	Thymus	Thymus
23	chr1:161017600-161021000	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr1:161017600-161024000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:161017600-161034400	Strong transcription	Fetal Thymus	thymus
26	chr1:161017800-161024400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr1:161017800-161026200	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:161018000-161025800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr1:161018000-161027400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:161018200-161026800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:161018400-161026000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
32	chr1:161018400-161026400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:161018400-161027400	Strong transcription	GM12878-XiMat	blood
34	chr1:161018600-161024200	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:161018600-161032400	Strong transcription	Primary B cells from cord blood	blood
36	chr1:161018600-161033600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:161018800-161022200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr1:161018800-161028200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
39	chr1:161019000-161021000	Strong transcription	Duodenum Mucosa	Duodenum
40	chr1:161019000-161026600	Strong transcription	Placenta	Placenta
41	chr1:161019200-161021000	Weak transcription	Pancreas	Pancrea
42	chr1:161019400-161021200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr1:161019400-161026000	Strong transcription	Spleen	Spleen
44	chr1:161019400-161029400	Strong transcription	Primary B cells from peripheral blood	blood
45	chr1:161019600-161021000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:161019600-161021000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:161019600-161021600	Genic enhancers	Monocytes-CD14+_RO01746	blood
48	chr1:161019600-161022600	Weak transcription	Adipose Nuclei	Adipose
49	chr1:161019600-161023400	Weak transcription	Brain Hippocampus Middle	brain
50	chr1:161019800-161025800	Weak transcription	Liver	Liver

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