Variant report

Variant	rs3098168
Chromosome Location	chr15:50751050-50751051
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	SPI1	chr15:50750884-50751315	GM12878	blood:	n/a	n/a
2	SPI1	chr15:50750980-50751351	GM12891	blood:	n/a	n/a
3	SPI1	chr15:50750942-50751310	GM12891	blood:	n/a	n/a
4	SPI1	chr15:50750979-50751269	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RNA5SP395	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11070776	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11070784	0.82[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs12050594	0.91[CHB][hapmap]
rs12593481	0.85[AMR][1000 genomes]
rs16963724	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs17645209	0.91[CHB][hapmap]
rs17645290	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2241769	0.88[CHB][hapmap]
rs2289108	0.85[CEU][hapmap]
rs28582911	0.80[AFR][1000 genomes]
rs28642809	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3098167	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3098169	0.90[CEU][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3098171	0.85[CEU][hapmap]
rs3098172	0.87[ASN][1000 genomes]
rs3098174	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3098177	0.85[CEU][hapmap];0.82[YRI][hapmap]
rs3098180	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs3098204	0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs3098205	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3131559	0.92[ASN][1000 genomes]
rs3131560	0.88[CEU][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3131562	0.85[CEU][hapmap];0.95[CHB][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3131564	0.87[ASN][1000 genomes]
rs3131565	0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs3131566	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3131567	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3131568	0.96[CEU][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3131571	0.91[ASN][1000 genomes]
rs3131572	0.90[ASN][1000 genomes]
rs3131574	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3131575	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs3131613	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs34546811	0.84[ASN][1000 genomes]
rs4318151	0.89[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56396299	0.88[ASN][1000 genomes]
rs61565615	0.86[ASN][1000 genomes]
rs7164347	0.88[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs7182407	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8026653	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv948579	chr15:50645530-51045564	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv524613	chr15:50656449-50868779	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv904210	chr15:50702058-50786024	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1040717	chr15:50715572-50846521	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS 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 target site	27 gene(s)	inside rSNPs	diseases
6	nsv1053966	chr15:50715572-51133186	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
7	nsv542383	chr15:50715572-51133186	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer 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	65 gene(s)	inside rSNPs	diseases
8	nsv1043805	chr15:50715572-51208891	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
9	nsv542384	chr15:50715572-51208891	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS 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 target site	82 gene(s)	inside rSNPs	diseases
10	nsv1049576	chr15:50744781-50843495	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
12	nsv1051990	chr15:50745814-51133186	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 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	chr15:50717600-50764600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:50717600-50774800	Weak transcription	Stomach Mucosa	stomach
3	chr15:50717800-50758800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:50718000-50755400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:50718000-50757000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:50722800-50764600	Weak transcription	Esophagus	oesophagus
7	chr15:50724600-50755800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr15:50724800-50764600	Weak transcription	Pancreas	Pancrea
9	chr15:50730800-50754200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr15:50733400-50785200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr15:50733600-50758200	Weak transcription	HMEC	breast
12	chr15:50733600-50758800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr15:50733800-50752800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:50733800-50755800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:50734000-50763200	Weak transcription	Brain Anterior Caudate	brain
16	chr15:50734000-50776400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr15:50734000-50785600	Weak transcription	Fetal Brain Male	brain
18	chr15:50734600-50752800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr15:50734600-50772600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr15:50735400-50764600	Weak transcription	Psoas Muscle	Psoas
21	chr15:50735600-50773000	Weak transcription	Brain Substantia Nigra	brain
22	chr15:50736200-50758600	Weak transcription	Right Ventricle	heart
23	chr15:50737200-50752600	Weak transcription	Lung	lung
24	chr15:50737200-50764800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr15:50737400-50755600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr15:50737400-50756800	Weak transcription	NHEK	skin
27	chr15:50737600-50751200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:50738200-50796800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr15:50738400-50755800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr15:50739400-50755200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:50740200-50777200	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr15:50740800-50770200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr15:50741800-50797000	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr15:50742400-50760000	Strong transcription	Duodenum Mucosa	Duodenum
35	chr15:50742600-50753600	Strong transcription	Primary T cells from cord blood	blood
36	chr15:50742600-50760000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr15:50744000-50782400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr15:50744000-50789000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr15:50744200-50754200	Weak transcription	NHDF-Ad	bronchial
40	chr15:50744800-50755600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr15:50745000-50752600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:50745400-50752800	Weak transcription	HSMMtube	muscle
43	chr15:50745400-50756000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr15:50745400-50771200	Weak transcription	NHLF	lung
45	chr15:50745600-50773800	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr15:50746000-50755800	Strong transcription	Fetal Intestine Small	intestine
47	chr15:50746200-50761000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr15:50746200-50794400	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr15:50746400-50767200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr15:50746600-50756000	Strong transcription	Primary T helper cells PMA-I stimulated	--

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