Variant report

Variant	rs59742225
Chromosome Location	chr4:6969942-6969943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:6962320..6964054-chr4:6967764..6970067,3	K562	blood:
2	chr4:6969313..6971458-chr4:6985802..6989389,3	K562	blood:
3	chr4:6968058..6971311-chr4:6972075..6975359,5	K562	blood:
4	chr4:6918816..6920459-chr4:6968873..6971872,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132405	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10000433	0.91[EUR][1000 genomes]
rs1048009	1.00[ASN][1000 genomes]
rs28384174	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28729690	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41410847	1.00[ASN][1000 genomes]
rs55633489	0.82[AMR][1000 genomes]
rs55659111	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55672215	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55740475	1.00[ASN][1000 genomes]
rs55833486	1.00[ASN][1000 genomes]
rs55913461	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55942328	0.86[AMR][1000 genomes]
rs56031152	1.00[ASN][1000 genomes]
rs56074877	0.86[AMR][1000 genomes]
rs56081162	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56094305	1.00[ASN][1000 genomes]
rs56178503	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56268690	0.87[EUR][1000 genomes]
rs56300156	0.86[AMR][1000 genomes]
rs56320732	1.00[ASN][1000 genomes]
rs56350643	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56400338	1.00[ASN][1000 genomes]
rs56903115	1.00[ASN][1000 genomes]
rs57454756	1.00[ASN][1000 genomes]
rs59683609	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59809420	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60048916	1.00[ASN][1000 genomes]
rs66519732	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66573146	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66611116	1.00[ASN][1000 genomes]
rs66645969	1.00[ASN][1000 genomes]
rs66712119	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66734745	1.00[ASN][1000 genomes]
rs66808450	1.00[ASN][1000 genomes]
rs66819208	1.00[ASN][1000 genomes]
rs66905212	1.00[ASN][1000 genomes]
rs67067921	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67245546	1.00[ASN][1000 genomes]
rs67252699	1.00[ASN][1000 genomes]
rs67315413	1.00[ASN][1000 genomes]
rs67321746	1.00[ASN][1000 genomes]
rs67405518	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67702333	1.00[ASN][1000 genomes]
rs67750430	1.00[ASN][1000 genomes]
rs67922134	1.00[ASN][1000 genomes]
rs67998004	1.00[ASN][1000 genomes]
rs68111914	1.00[ASN][1000 genomes]
rs6812391	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6812771	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68169399	1.00[ASN][1000 genomes]
rs6836225	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6838042	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838250	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6841389	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6851488	1.00[ASN][1000 genomes]
rs6855531	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088528	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088564	1.00[ASN][1000 genomes]
rs73199995	1.00[ASN][1000 genomes]
rs73202120	1.00[ASN][1000 genomes]
rs73202122	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7668802	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7675281	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686168	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686186	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9942188	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9992596	0.88[EUR][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	nsv878529	chr4:6883012-6983677	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:6945000-6970200	Weak transcription	Hela-S3	cervix
2	chr4:6955800-6976000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:6956000-6976000	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:6957600-6970400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:6957600-6973800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:6957600-6976000	Weak transcription	Fetal Lung	lung
7	chr4:6957800-6976000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:6958400-6975800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr4:6964200-6976000	Weak transcription	Brain Germinal Matrix	brain
10	chr4:6964800-6973400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:6965000-6976000	Weak transcription	A549	lung
12	chr4:6965200-6970400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr4:6965200-6971600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:6965200-6973400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:6965200-6976000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr4:6965200-6976000	Weak transcription	Stomach Mucosa	stomach
17	chr4:6965200-6976200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:6965400-6970000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:6965400-6973000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr4:6965400-6973000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:6965400-6973200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:6965400-6973400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr4:6965400-6973400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:6965400-6973600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr4:6965400-6974600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr4:6965400-6976000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:6965400-6976000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr4:6965400-6976000	Weak transcription	NHLF	lung
29	chr4:6965400-6976200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:6965400-6987800	Weak transcription	Small Intestine	intestine
31	chr4:6966200-6973800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:6966200-6976000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr4:6967000-6976000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr4:6967600-6973400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr4:6967600-6974400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr4:6967800-6973400	Weak transcription	Fetal Muscle Leg	muscle
37	chr4:6967800-6975000	Weak transcription	HSMMtube	muscle
38	chr4:6967800-6976000	Weak transcription	Fetal Kidney	kidney
39	chr4:6968000-6971600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr4:6968000-6973400	Weak transcription	Brain Angular Gyrus	brain
41	chr4:6968000-6987600	Weak transcription	HSMM	muscle
42	chr4:6968200-6976000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr4:6968400-6971400	Weak transcription	GM12878-XiMat	blood
44	chr4:6968400-6973400	Weak transcription	Brain Hippocampus Middle	brain
45	chr4:6968800-6971600	Strong transcription	HepG2	liver
46	chr4:6968800-6973800	Strong transcription	Primary T cells from cord blood	blood
47	chr4:6968800-6975000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr4:6968800-6975400	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr4:6969000-6970400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr4:6969000-6970800	Strong transcription	Duodenum Mucosa	Duodenum

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