Variant report

Variant	rs2576178
Chromosome Location	chr10:90343398-90343399
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	TCF12	chr10:90342301-90343540	A549	lung:	n/a	n/a
2	MAX	chr10:90342497-90343407	H1-hESC	embryonic stem cell:	n/a	chr10:90342538-90342548 chr10:90342660-90342669 chr10:90342661-90342670 chr10:90342661-90342670 chr10:90342659-90342672
3	RUNX3	chr10:90342485-90343422	GM12878	blood:	n/a	n/a
4	BCLAF1	chr10:90342505-90343467	GM12878	blood:	n/a	chr10:90343114-90343127
5	E2F6	chr10:90342409-90343473	H1-hESC	embryonic stem cell:	n/a	chr10:90343369-90343378 chr10:90343100-90343112
6	CTCF	chr10:90342780-90343408	MCF-7	breast:	n/a	chr10:90343091-90343109 chr10:90343094-90343107
7	RELA	chr10:90342620-90343445	GM15510	blood:	n/a	n/a
8	ZNF143	chr10:90342469-90343597	GM12878	blood:	n/a	chr10:90342641-90342651
9	POLR2A	chr10:90342369-90343523	GM12891	blood:	n/a	n/a
10	TAF1	chr10:90342495-90343480	H1-hESC	embryonic stem cell:	n/a	n/a
11	NFIC	chr10:90342462-90343427	GM12878	blood:	n/a	n/a
12	GABPA	chr10:90342271-90343470	MCF-7	breast:	n/a	n/a
13	ZNF143	chr10:90342750-90343612	H1-hESC	embryonic stem cell:	n/a	n/a
14	RUNX3	chr10:90342599-90343463	GM12878	blood:	n/a	n/a
15	MAX	chr10:90342290-90343479	A549	lung:	n/a	chr10:90342538-90342548 chr10:90342660-90342669 chr10:90342661-90342670 chr10:90342661-90342670 chr10:90342659-90342672
16	RCOR1	chr10:90342649-90343690	GM12878	blood:	n/a	n/a
17	WRNIP1	chr10:90343213-90343457	GM12878	blood:	n/a	n/a
18	CTCF	chr10:90343260-90343410	AG04449	skin:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LIPJ-2	chr10:90343084-90344727	NONHSAT015473

Variant related genes	Relation type
LIPJ	TF binding region
RNLS	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10788608	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10887837	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs10887839	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10887840	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs10887841	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs11202772	0.80[JPT][hapmap]
rs11202781	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1409137	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1555841	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2274312	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2296545	0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2576168	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs2765446	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2765452	0.94[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs7476392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948664	chr10:90076715-90517150	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv430254	chr10:90265420-90500520	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1044680	chr10:90316066-90466092	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv540740	chr10:90316066-90466092	Active TSS Enhancers Flanking Active TSS Weak transcription 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	9 gene(s)	inside rSNPs	diseases
6	nsv1037657	chr10:90329910-90367890	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv551839	chr10:90334835-90422136	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2576178	LIPN	cis	cerebellum	SCAN
rs2576178	LIPJ	cis	parietal	SCAN
rs2576178	KIF20B	cis	parietal	SCAN
rs2576178	ANKRD22	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90341800-90343600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr10:90341800-90343800	Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr10:90341800-90343800	Active TSS	Stomach Smooth Muscle	stomach
4	chr10:90342000-90343600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr10:90342000-90343600	Active TSS	Fetal Lung	lung
6	chr10:90342000-90343800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr10:90342000-90343800	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr10:90342000-90343800	Active TSS	Rectal Smooth Muscle	rectum
9	chr10:90342000-90343800	Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr10:90342200-90343400	Active TSS	Brain Hippocampus Middle	brain
11	chr10:90342200-90343400	Active TSS	Duodenum Mucosa	Duodenum
12	chr10:90342200-90343400	Active TSS	K562	blood
13	chr10:90342200-90343600	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr10:90342200-90343600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr10:90342200-90343600	Active TSS	Brain Angular Gyrus	brain
16	chr10:90342200-90343600	Active TSS	Brain Germinal Matrix	brain
17	chr10:90342200-90343600	Active TSS	Fetal Intestine Large	intestine
18	chr10:90342200-90343600	Active TSS	Thymus	Thymus
19	chr10:90342200-90343800	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr10:90342200-90343800	Active TSS	H1 Cell Line	embryonic stem cell
21	chr10:90342200-90343800	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr10:90342200-90343800	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr10:90342200-90343800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr10:90342200-90343800	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr10:90342200-90343800	Active TSS	Fetal Brain Female	brain
26	chr10:90342200-90343800	Active TSS	Fetal Kidney	kidney
27	chr10:90342200-90343800	Active TSS	Right Atrium	heart
28	chr10:90342200-90343800	Active TSS	A549	lung
29	chr10:90342200-90343800	Active TSS	NHDF-Ad	bronchial
30	chr10:90342200-90344000	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr10:90342400-90343400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr10:90342400-90343400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr10:90342400-90343400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr10:90342400-90343400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr10:90342400-90343400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr10:90342400-90343400	Active TSS	Brain Anterior Caudate	brain
37	chr10:90342400-90343400	Active TSS	Brain Cingulate Gyrus	brain
38	chr10:90342400-90343400	Active TSS	Brain Substantia Nigra	brain
39	chr10:90342400-90343400	Active TSS	Colon Smooth Muscle	Colon
40	chr10:90342400-90343400	Active TSS	Fetal Intestine Small	intestine
41	chr10:90342400-90343400	Active TSS	Pancreas	Pancrea
42	chr10:90342400-90343400	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr10:90342400-90343600	Active TSS	H9 Cell Line	embryonic stem cell
44	chr10:90342400-90343600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr10:90342400-90343600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr10:90342400-90343600	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr10:90342400-90343600	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr10:90342400-90343600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr10:90342400-90343600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr10:90342400-90343600	Active TSS	Breast Myoepithelial Primary Cells	Breast

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