Variant report

Variant	rs11249553
Chromosome Location	chr5:178049188-178049189
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	CTCF	chr5:178049166-178049237	K562	blood:	n/a	n/a
2	ZNF384	chr5:178049126-178049220	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:177767131..177770109-chr5:178047191..178050111,2	MCF-7	breast:

Variant related genes	Relation type
RN7SKP70	TF binding region
CLK4	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11249554	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11249556	0.82[EUR][1000 genomes]
rs11737903	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11740194	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11746942	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11747742	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12514311	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12518589	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13155255	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13156622	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35460909	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35522922	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36008351	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs501721	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs519984	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs530542	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs574103	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs576097	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs584415	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs596780	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs602019	0.97[ASN][1000 genomes]
rs602451	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628857	0.84[AMR][1000 genomes]
rs643936	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs649585	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6882079	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6886390	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721144	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7702727	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7732660	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11249553	CLK4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178024000-178050000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr5:178026200-178050200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:178026400-178050000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:178026400-178050200	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr5:178026400-178050200	Strong transcription	Fetal Lung	lung
6	chr5:178026400-178050400	Strong transcription	Placenta	Placenta
7	chr5:178026400-178050400	Strong transcription	Fetal Thymus	thymus
8	chr5:178026400-178050400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr5:178026400-178050600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:178026400-178050800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:178026800-178050400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:178027000-178049800	Strong transcription	Dnd41	blood
13	chr5:178027000-178050600	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr5:178027400-178049400	Strong transcription	GM12878-XiMat	blood
15	chr5:178027600-178050000	Strong transcription	Primary hematopoietic stem cells	blood
16	chr5:178027600-178050400	Strong transcription	Primary B cells from peripheral blood	blood
17	chr5:178028000-178050400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr5:178028000-178050400	Strong transcription	NH-A	brain
19	chr5:178028200-178049600	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:178028200-178050200	Strong transcription	Fetal Intestine Large	intestine
21	chr5:178028400-178049800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:178028400-178050200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:178028400-178050400	Strong transcription	Duodenum Mucosa	Duodenum
24	chr5:178028800-178050400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:178030200-178049800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:178030400-178050400	Strong transcription	HSMM	muscle
27	chr5:178030600-178050400	Strong transcription	Osteobl	bone
28	chr5:178031800-178052800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:178033000-178050600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:178034400-178050200	Strong transcription	Liver	Liver
31	chr5:178035000-178050400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:178035000-178050400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:178035800-178052000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr5:178036000-178050200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:178036400-178049600	Strong transcription	Thymus	Thymus
36	chr5:178036400-178050200	Strong transcription	HMEC	breast
37	chr5:178037000-178049800	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr5:178037000-178050000	Strong transcription	Stomach Smooth Muscle	stomach
39	chr5:178037000-178050200	Strong transcription	Fetal Brain Female	brain
40	chr5:178037000-178050400	Strong transcription	Brain Substantia Nigra	brain
41	chr5:178037200-178049200	Strong transcription	Brain Anterior Caudate	brain
42	chr5:178037200-178050200	Strong transcription	Primary B cells from cord blood	blood
43	chr5:178037200-178050400	Strong transcription	Fetal Kidney	kidney
44	chr5:178037400-178050200	Strong transcription	A549	lung
45	chr5:178037400-178050400	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr5:178037400-178050600	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr5:178037800-178050800	Weak transcription	Stomach Mucosa	stomach
48	chr5:178038000-178049600	Strong transcription	Fetal Brain Male	brain
49	chr5:178038000-178050200	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr5:178038000-178050400	Strong transcription	K562	blood

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