Variant report

Variant	rs4925173
Chromosome Location	chr17:18229057-18229058
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:18228483..18234046-chr17:18234126..18237765,7	K562	blood:
2	chr17:18217609..18225680-chr17:18226125..18232187,14	K562	blood:
3	chr17:18229026..18230559-chr17:18233647..18235294,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SMCR8-1	chr17:18227536-18229211	ENSG00000267350.2
2	lnc-SMCR8-1	chr17:18228890-18231369	NONHSAT146178

Variant related genes	Relation type
ENSG00000176994	Chromatin interaction
ENSG00000177302	Chromatin interaction
ENSG00000176974	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11540888	1.00[ASN][1000 genomes]
rs11870681	1.00[ASN][1000 genomes]
rs16961058	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16961112	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2125154	1.00[CEU][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28671051	0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4924848	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925170	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925174	1.00[CEU][hapmap]
rs4925175	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925180	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55973639	1.00[ASN][1000 genomes]
rs61753153	1.00[ASN][1000 genomes]
rs6502648	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215491	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7222589	1.00[ASN][1000 genomes]
rs73980813	1.00[ASN][1000 genomes]
rs73980819	1.00[ASN][1000 genomes]
rs73980849	1.00[ASN][1000 genomes]
rs73980856	1.00[ASN][1000 genomes]
rs73980857	1.00[ASN][1000 genomes]
rs8074858	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8080285	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8082574	1.00[ASN][1000 genomes]
rs9893254	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9894005	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9894616	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9897954	1.00[CEU][hapmap]
rs9902011	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9902498	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9903235	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9903762	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9904323	1.00[CEU][hapmap]
rs9913916	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9915858	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	nsv833386	chr17:18170261-18332726	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv1057081	chr17:18171516-18256347	Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv543247	chr17:18171516-18256347	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS 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 miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1062368	chr17:18180747-18259234	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv833387	chr17:18200081-18378155	Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	esv1806346	chr17:18200081-18446384	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	esv1812661	chr17:18200081-18446384	Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv428333	chr17:18200081-18446384	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
13	nsv427992	chr17:18200081-19192047	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
14	esv1004827	chr17:18227768-18233875	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18219400-18266000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:18222400-18266200	Weak transcription	Small Intestine	intestine
3	chr17:18222600-18240800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr17:18222600-18243200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr17:18222800-18236800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr17:18223400-18235400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr17:18223600-18240800	Strong transcription	Fetal Muscle Leg	muscle
8	chr17:18223600-18265400	Strong transcription	Fetal Stomach	stomach
9	chr17:18223800-18229200	Strong transcription	NHEK	skin
10	chr17:18223800-18236800	Strong transcription	Primary T cells from cord blood	blood
11	chr17:18223800-18236800	Strong transcription	Lung	lung
12	chr17:18223800-18240800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr17:18223800-18253600	Strong transcription	Thymus	Thymus
14	chr17:18224000-18231000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
15	chr17:18224000-18236600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr17:18224000-18236600	Strong transcription	Fetal Intestine Large	intestine
17	chr17:18224000-18236800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr17:18224000-18240800	Strong transcription	Dnd41	blood
19	chr17:18224200-18229400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr17:18224200-18230200	Strong transcription	Brain Anterior Caudate	brain
21	chr17:18224200-18234600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr17:18224200-18235600	Strong transcription	Esophagus	oesophagus
23	chr17:18224200-18236200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr17:18224200-18236400	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr17:18224200-18236600	Strong transcription	Rectal Smooth Muscle	rectum
26	chr17:18224200-18236600	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr17:18224200-18240800	Strong transcription	Fetal Muscle Trunk	muscle
28	chr17:18224200-18253000	Weak transcription	Fetal Heart	heart
29	chr17:18224400-18249400	Weak transcription	K562	blood
30	chr17:18224600-18236400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr17:18224800-18229600	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr17:18224800-18236600	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr17:18224800-18236800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr17:18224800-18240600	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr17:18224800-18240800	Strong transcription	Fetal Brain Female	brain
36	chr17:18224800-18241000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr17:18224800-18241000	Strong transcription	Adipose Nuclei	Adipose
38	chr17:18225000-18233000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr17:18225400-18240800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr17:18225600-18236800	Strong transcription	Brain Cingulate Gyrus	brain
41	chr17:18225600-18239200	Strong transcription	Placenta	Placenta
42	chr17:18225600-18240400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr17:18225600-18241600	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr17:18225800-18229200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr17:18225800-18232400	Strong transcription	Primary hematopoietic stem cells	blood
46	chr17:18225800-18236000	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr17:18225800-18236600	Strong transcription	Brain Germinal Matrix	brain
48	chr17:18225800-18236600	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr17:18225800-18236600	Strong transcription	Right Ventricle	heart
50	chr17:18225800-18236800	Strong transcription	Duodenum Mucosa	Duodenum

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