Variant report

Variant	rs501721
Chromosome Location	chr5:178035585-178035586
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:178029713..178031440-chr5:178034410..178036578,2	K562	blood:
2	chr5:178035433..178037862-chr5:178050507..178052447,2	K562	blood:
3	chr5:178034097..178036598-chr5:178052522..178054162,2	MCF-7	breast:
4	chr5:178026410..178028805-chr5:178033864..178036012,2	K562	blood:
5	chr5:178035506..178039480-chr5:178042939..178045569,4	MCF-7	breast:
6	chr5:178034173..178036020-chr5:178052814..178054852,2	K562	blood:

Variant related genes	Relation type
ENSG00000113240	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11249553	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11249554	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11249556	0.80[EUR][1000 genomes]
rs11737903	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11740194	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11746942	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11747742	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12514311	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12518589	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13155255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13156622	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs262027	0.90[CHB][hapmap]
rs35460909	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35522922	0.84[EUR][1000 genomes]
rs36008351	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs519984	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs530542	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs555417	0.94[JPT][hapmap];1.00[YRI][hapmap]
rs574103	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs576097	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs584415	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs596780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs602019	0.98[ASN][1000 genomes]
rs602451	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs628857	0.92[CEU][hapmap];0.86[AMR][1000 genomes]
rs643936	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs649585	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6882079	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6886390	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs721144	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7700943	0.82[CEU][hapmap]
rs7702727	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7724406	0.82[CEU][hapmap]
rs7732660	0.92[CEU][hapmap];0.94[JPT][hapmap];0.86[AMR][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	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	nsv883214	chr5:177876309-178047217	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs501721	CLK4	Cis_1M	lymphoblastoid	RTeQTL
rs501721	CLK4	cis	normal skin	skin_eQTL
rs501721	CLK4	cis	lesional skin	skin_eQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178018200-178043200	Weak transcription	Aorta	Aorta
2	chr5:178019400-178036800	Weak transcription	Psoas Muscle	Psoas
3	chr5:178022400-178038600	Weak transcription	Small Intestine	intestine
4	chr5:178023200-178046000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr5:178024000-178050000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:178024400-178046000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr5:178024600-178035800	Strong transcription	Primary B cells from cord blood	blood
8	chr5:178024600-178037000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr5:178026200-178050200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:178026400-178048400	Strong transcription	Fetal Muscle Trunk	muscle
11	chr5:178026400-178050000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:178026400-178050200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr5:178026400-178050200	Strong transcription	Fetal Lung	lung
14	chr5:178026400-178050400	Strong transcription	Placenta	Placenta
15	chr5:178026400-178050400	Strong transcription	Fetal Thymus	thymus
16	chr5:178026400-178050400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr5:178026400-178050600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:178026400-178050800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr5:178026800-178035800	Strong transcription	Primary T cells from cord blood	blood
20	chr5:178026800-178036200	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr5:178026800-178050400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr5:178027000-178047200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr5:178027000-178049800	Strong transcription	Dnd41	blood
24	chr5:178027000-178050600	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr5:178027400-178036200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:178027400-178036400	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr5:178027400-178049400	Strong transcription	GM12878-XiMat	blood
28	chr5:178027600-178035800	Strong transcription	Brain Anterior Caudate	brain
29	chr5:178027600-178036000	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr5:178027600-178050000	Strong transcription	Primary hematopoietic stem cells	blood
31	chr5:178027600-178050400	Strong transcription	Primary B cells from peripheral blood	blood
32	chr5:178028000-178036200	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr5:178028000-178036200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr5:178028000-178036200	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr5:178028000-178050400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr5:178028000-178050400	Strong transcription	NH-A	brain
37	chr5:178028200-178046000	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr5:178028200-178049600	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr5:178028200-178050200	Strong transcription	Fetal Intestine Large	intestine
40	chr5:178028400-178046800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr5:178028400-178049800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr5:178028400-178050200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr5:178028400-178050400	Strong transcription	Duodenum Mucosa	Duodenum
44	chr5:178028600-178035800	Strong transcription	Fetal Brain Female	brain
45	chr5:178028600-178036200	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr5:178028600-178046200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr5:178028600-178046200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr5:178028800-178046000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr5:178028800-178050400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr5:178029000-178047200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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