Variant report

Variant	rs55688744
Chromosome Location	chr3:160944222-160944223
allele	A/G
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	PRDM1	chr3:160944220-160944505	Hela-S3	cervix:	n/a	chr3:160944319-160944333 chr3:160944318-160944333 chr3:160944323-160944332 chr3:160944319-160944332
2	POLR2A	chr3:160943332-160945070	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:160943414..160948630-chr3:161124537..161130455,7	MCF-7	breast:
2	chr3:160942925..160944989-chr3:161039772..161043116,3	MCF-7	breast:
3	chr3:160818503..160825890-chr3:160937051..160945986,18	MCF-7	breast:
4	chr3:160943734..160947750-chr3:160947797..160950520,6	MCF-7	breast:
5	chr3:160934982..160947568-chr3:161079696..161093037,40	MCF-7	breast:
6	chr3:160819564..160821281-chr3:160942870..160944755,2	MCF-7	breast:
7	chr3:160936365..160960187-chr3:161078472..161094658,51	MCF-7	breast:
8	chr3:160944121..160946276-chr3:160955129..160957203,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271052	TF binding region
ENSG00000169255	Chromatin interaction
ENSG00000169251	Chromatin interaction
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10936223	0.88[AMR][1000 genomes]
rs10936224	0.91[AMR][1000 genomes]
rs1154701	0.85[EUR][1000 genomes]
rs12486253	0.95[EUR][1000 genomes]
rs12495310	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12631850	0.88[AMR][1000 genomes]
rs13083229	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1478568	0.95[EUR][1000 genomes]
rs1599381	0.81[AMR][1000 genomes]
rs4290817	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4470535	0.96[EUR][1000 genomes]
rs4518145	0.88[EUR][1000 genomes]
rs4560315	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4618258	0.83[AMR][1000 genomes]
rs4856714	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4856738	0.96[EUR][1000 genomes]
rs4856739	0.86[EUR][1000 genomes]
rs4856767	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4856768	0.95[EUR][1000 genomes]
rs6441370	0.85[EUR][1000 genomes]
rs6441371	0.83[EUR][1000 genomes]
rs6768818	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6774276	0.88[EUR][1000 genomes]
rs6789244	0.81[AMR][1000 genomes]
rs6789388	0.86[EUR][1000 genomes]
rs6791213	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6794601	0.80[EUR][1000 genomes]
rs6809256	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7611367	0.85[EUR][1000 genomes]
rs7613227	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7613358	0.98[EUR][1000 genomes]
rs7627528	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7630768	0.81[AMR][1000 genomes]
rs7632797	0.85[EUR][1000 genomes]
rs7633186	0.85[EUR][1000 genomes]
rs7636941	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7652267	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs899275	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9809522	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9815222	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9834659	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9839527	0.95[EUR][1000 genomes]
rs9864752	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9879687	0.88[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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55688744	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160939800-160995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:160940000-160971600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:160940000-160977400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:160940200-160965400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:160940800-160946600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:160940800-160946600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:160940800-160956000	Weak transcription	Colonic Mucosa	Colon
8	chr3:160941000-160946400	Weak transcription	Brain Substantia Nigra	brain
9	chr3:160941000-160946400	Weak transcription	Lung	lung
10	chr3:160941000-160946400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:160941000-160946600	Weak transcription	Thymus	Thymus
12	chr3:160941000-160956000	Weak transcription	Esophagus	oesophagus
13	chr3:160941000-160969600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:160941000-160970200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:160941000-160974800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:160941000-160983000	Weak transcription	Spleen	Spleen
17	chr3:160941000-160984600	Weak transcription	Small Intestine	intestine
18	chr3:160941000-160993400	Weak transcription	Pancreas	Pancrea
19	chr3:160941200-160944800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:160941200-160945800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:160941200-160946000	Weak transcription	HSMMtube	muscle
22	chr3:160941200-160946400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr3:160941200-160946800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:160941200-160968600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr3:160941200-160969800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:160941200-160973400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:160941400-160971800	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:160941600-160944600	Weak transcription	NHLF	lung
29	chr3:160941600-160944800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:160941600-160946400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:160941600-160946400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:160941600-160969800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr3:160941600-160975400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:160941800-160944400	Weak transcription	A549	lung
35	chr3:160941800-160945200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:160941800-160946400	Weak transcription	Psoas Muscle	Psoas
37	chr3:160941800-160947200	Weak transcription	Fetal Brain Female	brain
38	chr3:160941800-160948000	Weak transcription	Brain Germinal Matrix	brain
39	chr3:160941800-160948200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:160941800-160948600	Weak transcription	Fetal Kidney	kidney
41	chr3:160941800-160949000	Weak transcription	Fetal Heart	heart
42	chr3:160941800-160951200	Weak transcription	Brain Anterior Caudate	brain
43	chr3:160941800-160956000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr3:160941800-160975200	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr3:160942000-160944400	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr3:160942000-160948200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:160942000-160950200	Strong transcription	Fetal Muscle Leg	muscle
48	chr3:160942000-160954400	Strong transcription	Placenta	Placenta
49	chr3:160942000-160964000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:160942200-160944400	Enhancers	Stomach Mucosa	stomach

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