Variant report

Variant	rs6554344
Chromosome Location	chr4:57179649-57179650
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:56814043..56816033-chr4:57177641..57180439,2	K562	blood:
2	chr4:57175601..57178505-chr4:57178570..57181893,3	K562	blood:

Variant related genes	Relation type
ENSG00000174799	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10008223	0.91[EUR][1000 genomes]
rs10010544	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10013402	0.91[EUR][1000 genomes]
rs10434444	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs10461357	0.85[EUR][1000 genomes]
rs11133443	0.92[CEU][hapmap]
rs1124569	0.85[EUR][1000 genomes]
rs11723782	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12498340	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs12512742	0.82[EUR][1000 genomes]
rs17086696	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs1983378	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs2030366	0.86[EUR][1000 genomes]
rs2049088	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2271925	0.86[EUR][1000 genomes]
rs28510634	0.91[EUR][1000 genomes]
rs3796548	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs3822001	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs4263445	0.86[EUR][1000 genomes]
rs4864579	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs4864580	0.89[EUR][1000 genomes]
rs4865088	0.92[EUR][1000 genomes]
rs4865089	0.89[EUR][1000 genomes]
rs4865092	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs56066795	0.86[EUR][1000 genomes]
rs56356367	0.81[EUR][1000 genomes]
rs56887793	0.89[EUR][1000 genomes]
rs59997251	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61032900	0.92[EUR][1000 genomes]
rs67957495	0.92[EUR][1000 genomes]
rs6820279	0.92[EUR][1000 genomes]
rs6836118	0.92[CEU][hapmap]
rs7670991	0.91[EUR][1000 genomes]
rs7696808	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8340	0.92[CEU][hapmap];0.91[EUR][1000 genomes]

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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv3415289	chr4:57063312-57236755	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6554344	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57162800-57189400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr4:57163000-57184000	Weak transcription	Right Atrium	heart
3	chr4:57163400-57180400	Weak transcription	Pancreas	Pancrea
4	chr4:57167600-57203400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:57167800-57218600	Weak transcription	Small Intestine	intestine
6	chr4:57171000-57187400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:57172000-57180000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:57172000-57204000	Weak transcription	Stomach Mucosa	stomach
9	chr4:57172600-57179800	Weak transcription	Placenta	Placenta
10	chr4:57172600-57180000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:57173000-57180200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:57173200-57202800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr4:57173600-57180000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:57173800-57182600	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr4:57173800-57185200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:57174400-57195000	Strong transcription	Fetal Intestine Small	intestine
17	chr4:57174400-57203800	Weak transcription	Fetal Kidney	kidney
18	chr4:57174600-57180200	Strong transcription	Fetal Intestine Large	intestine
19	chr4:57174600-57182200	Weak transcription	HepG2	liver
20	chr4:57174600-57197200	Strong transcription	Duodenum Mucosa	Duodenum
21	chr4:57176000-57183400	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr4:57176000-57190000	Weak transcription	Gastric	stomach
23	chr4:57176400-57180400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr4:57176600-57180400	Weak transcription	Thymus	Thymus
25	chr4:57176600-57183200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr4:57177200-57183000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:57177400-57185200	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr4:57177600-57181200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:57177600-57182200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:57177600-57215400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr4:57177800-57183400	Strong transcription	Colonic Mucosa	Colon
32	chr4:57177800-57184000	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr4:57177800-57184200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr4:57178000-57190400	Weak transcription	Brain Angular Gyrus	brain
35	chr4:57178200-57183600	Strong transcription	Fetal Stomach	stomach
36	chr4:57178200-57184400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr4:57178200-57189400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr4:57178200-57189800	Weak transcription	Brain Anterior Caudate	brain
39	chr4:57178200-57190000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr4:57178200-57190200	Weak transcription	Brain Substantia Nigra	brain
41	chr4:57178200-57211800	Weak transcription	Brain Hippocampus Middle	brain
42	chr4:57178400-57182800	Weak transcription	Fetal Lung	lung
43	chr4:57178400-57183200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr4:57178600-57190200	Weak transcription	Fetal Brain Male	brain
45	chr4:57178800-57181000	Strong transcription	Primary hematopoietic stem cells	blood
46	chr4:57178800-57181800	Strong transcription	Fetal Muscle Leg	muscle
47	chr4:57178800-57182200	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr4:57178800-57183200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:57178800-57187000	Strong transcription	Fetal Brain Female	brain
50	chr4:57179000-57180600	Strong transcription	HUES6 Cell Line	embryonic stem cell

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