Variant report

Variant	rs35549743
Chromosome Location	chr6:13294354-13294355
allele	C/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	POLR2A	chr6:13294342-13294362	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr6:13294133-13294393	MCF-7	breast:	n/a	n/a
3	POLR2A	chr6:13294066-13294395	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13276714..13280149-chr6:13292500..13295672,4	K562	blood:
2	chr6:13288763..13290813-chr6:13291778..13294382,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272379	TF binding region
ENSG00000272379	Chromatin interaction
ENSG00000112137	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1223397	0.80[EUR][1000 genomes]
rs1223399	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1223400	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1223401	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1223402	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1223403	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1232392	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13191897	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13205692	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17700321	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17767967	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs202029	0.90[ASN][1000 genomes]
rs202032	0.90[ASN][1000 genomes]
rs2048552	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs20499	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs20500	0.96[EUR][1000 genomes]
rs34505804	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35511719	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs364493	0.92[ASN][1000 genomes]
rs3734878	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3817737	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3817738	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3817741	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3817742	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71530382	0.88[ASN][1000 genomes]
rs9381884	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9395602	0.87[AMR][1000 genomes];0.91[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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 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	chr6:13274600-13302000	Weak transcription	Small Intestine	intestine
2	chr6:13285400-13302400	Weak transcription	HUVEC	blood vessel
3	chr6:13287000-13303600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:13287400-13294400	Weak transcription	Fetal Kidney	kidney
5	chr6:13287800-13295200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr6:13287800-13298200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr6:13288000-13294600	Weak transcription	Fetal Brain Male	brain
8	chr6:13288000-13296200	Strong transcription	Primary B cells from peripheral blood	blood
9	chr6:13288200-13295400	Weak transcription	Fetal Heart	heart
10	chr6:13288200-13296400	Strong transcription	GM12878-XiMat	blood
11	chr6:13288400-13294800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:13288400-13302600	Weak transcription	Hela-S3	cervix
13	chr6:13288400-13302800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr6:13288600-13295000	Strong transcription	Primary B cells from cord blood	blood
15	chr6:13288600-13295000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:13288600-13296400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:13288600-13302400	Strong transcription	Fetal Brain Female	brain
18	chr6:13288600-13302600	Strong transcription	Fetal Muscle Leg	muscle
19	chr6:13288600-13321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr6:13288600-13326400	Strong transcription	Primary T cells from cord blood	blood
21	chr6:13289000-13295800	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr6:13289000-13299800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:13289600-13294600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:13289800-13327000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:13290200-13302800	Weak transcription	NHEK	skin
26	chr6:13290400-13296200	Strong transcription	Fetal Thymus	thymus
27	chr6:13290400-13296800	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr6:13290400-13310400	Strong transcription	Dnd41	blood
29	chr6:13290600-13295600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:13290600-13296800	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr6:13290600-13302800	Weak transcription	Stomach Mucosa	stomach
32	chr6:13290800-13296400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr6:13291000-13295800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:13291000-13297200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:13291000-13297400	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr6:13291000-13302800	Strong transcription	Fetal Stomach	stomach
37	chr6:13291200-13303000	Strong transcription	Fetal Intestine Small	intestine
38	chr6:13291200-13310400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr6:13291400-13296400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr6:13291400-13297800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr6:13291400-13299600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr6:13291400-13300200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:13291400-13303600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:13291600-13294400	Strong transcription	Spleen	Spleen
45	chr6:13291600-13294800	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr6:13291600-13295000	Strong transcription	Aorta	Aorta
47	chr6:13291600-13295600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:13291600-13295600	Strong transcription	Brain Anterior Caudate	brain
49	chr6:13291600-13295600	Strong transcription	HSMMtube	muscle
50	chr6:13291600-13295800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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