Variant report

Variant	rs1555430
Chromosome Location	chr6:24780263-24780264
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:24760069..24763397-chr6:24777478..24780398,3	K562	blood:
2	chr6:24666490..24670247-chr6:24774150..24780460,9	K562	blood:
3	chr6:24711892..24724164-chr6:24769415..24786834,81	K562	blood:
4	chr6:24699907..24702798-chr6:24778653..24782809,3	K562	blood:
5	chr6:24707645..24711659-chr6:24779375..24784848,6	K562	blood:
6	chr6:24715365..24725462-chr6:24770390..24783002,86	K562	blood:
7	chr6:24720478..24722311-chr6:24779195..24782638,3	MCF-7	breast:
8	chr6:24773976..24777184-chr6:24777863..24780331,3	MCF-7	breast:
9	chr6:24778637..24781525-chr6:24789510..24791363,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000112312	Chromatin interaction
ENSG00000272345	Chromatin interaction
ENSG00000112304	Chromatin interaction
ENSG00000111802	Chromatin interaction
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10946722	1.00[LWK][hapmap]
rs12214068	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064976	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2145752	0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2754776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2754777	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2817728	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2817732	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2817739	0.87[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3777663	1.00[LWK][hapmap]
rs3813687	1.00[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830609	chr6:24712086-24896647	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv428474	chr6:24714157-24797977	Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers 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	65 gene(s)	inside rSNPs	diseases
3	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv5227	chr6:24774149-24824012	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS 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 miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv508396	chr6:24779648-24846309	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1555430	HIST1H4G	cis	cerebellum	SCAN
rs1555430	CMAH	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24774600-24780400	Active TSS	Fetal Stomach	stomach
2	chr6:24775800-24780400	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr6:24776200-24782000	Weak transcription	Fetal Brain Male	brain
4	chr6:24776200-24787000	Weak transcription	Aorta	Aorta
5	chr6:24776400-24803200	Weak transcription	HSMMtube	muscle
6	chr6:24776400-24807400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr6:24776600-24786800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:24776800-24788000	Weak transcription	Colon Smooth Muscle	Colon
9	chr6:24776800-24788400	Weak transcription	Esophagus	oesophagus
10	chr6:24776800-24790600	Weak transcription	Right Ventricle	heart
11	chr6:24776800-24807600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:24777000-24780400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:24777000-24780800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr6:24777000-24781000	Weak transcription	Fetal Muscle Leg	muscle
15	chr6:24777000-24781000	Weak transcription	Thymus	Thymus
16	chr6:24777000-24781200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:24777000-24781600	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr6:24777000-24781600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr6:24777000-24781800	Weak transcription	Placenta	Placenta
20	chr6:24777000-24782000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:24777000-24782000	Weak transcription	Lung	lung
22	chr6:24777000-24782200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr6:24777000-24784400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr6:24777000-24786000	Weak transcription	Brain Substantia Nigra	brain
25	chr6:24777000-24786000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr6:24777000-24786400	Weak transcription	Ovary	ovary
27	chr6:24777000-24787000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:24777000-24787000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:24777000-24788400	Weak transcription	Colonic Mucosa	Colon
30	chr6:24777000-24788800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:24777000-24789000	Weak transcription	Gastric	stomach
32	chr6:24777000-24790800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr6:24777000-24791000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr6:24777000-24791000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr6:24777000-24797000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:24777000-24801200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr6:24777000-24802400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:24777000-24805000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr6:24777000-24806200	Weak transcription	Spleen	Spleen
40	chr6:24777000-24808000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr6:24777000-24809400	Weak transcription	Brain Germinal Matrix	brain
42	chr6:24777000-24811600	Weak transcription	Brain Hippocampus Middle	brain
43	chr6:24777000-24847600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:24777000-24859600	Weak transcription	Psoas Muscle	Psoas
45	chr6:24777200-24781000	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr6:24777200-24783000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr6:24777200-24783000	Weak transcription	Adipose Nuclei	Adipose
48	chr6:24777200-24784400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr6:24777200-24784600	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr6:24777200-24787400	Weak transcription	Fetal Brain Female	brain

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