Variant report

Variant	rs793515
Chromosome Location	chr10:98988469-98988470
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:98986271..98988962-chr10:98994711..98997131,2	K562	blood:
2	chr10:98980598..98984541-chr10:98986940..98989319,3	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11189121	0.84[CEU][hapmap];0.86[TSI][hapmap]
rs11189131	0.81[ASW][hapmap];0.81[CEU][hapmap]
rs1147600	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12240590	0.84[CEU][hapmap];0.86[TSI][hapmap]
rs1253394	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1253401	0.89[CEU][hapmap]
rs1253404	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1253427	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13439	0.84[CEU][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes]
rs1468069	0.81[EUR][1000 genomes]
rs1687369	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1687372	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2297987	0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs2484880	0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2484881	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34787876	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61861820	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs701810	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs701812	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs701813	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs701814	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs701815	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs701816	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs701817	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs701819	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs701821	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs7915926	0.95[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs793516	0.90[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs793517	0.90[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs793518	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793519	0.89[CEU][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap]
rs793520	0.84[CEU][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs793524	0.84[CEU][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap]
rs946981	0.84[CEU][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][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	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1041614	chr10:98928281-99083056	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv3361060	chr10:98939103-99025202	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1045553	chr10:98944397-99122203	Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv540750	chr10:98944397-99122203	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv1797410	chr10:98983785-99041740	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1040903	chr10:98986382-99047475	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs793515	TLX1	cis	cerebellum	SCAN
rs793515	RRP12	cis	parietal	SCAN
rs793515	HELLS	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98973800-99019000	Weak transcription	HepG2	liver
2	chr10:98976000-99011400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr10:98977200-99023800	Weak transcription	Colonic Mucosa	Colon
4	chr10:98977400-99027000	Weak transcription	Right Ventricle	heart
5	chr10:98978200-99003400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr10:98978200-99003600	Weak transcription	NHEK	skin
7	chr10:98978600-98988800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr10:98978600-99019000	Weak transcription	HSMMtube	muscle
9	chr10:98978600-99030400	Weak transcription	NH-A	brain
10	chr10:98978600-99037400	Weak transcription	HSMM	muscle
11	chr10:98978600-99051800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr10:98979000-98990400	Strong transcription	Fetal Thymus	thymus
13	chr10:98979000-99027400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr10:98979400-98989600	Weak transcription	NHLF	lung
15	chr10:98979400-99000600	Strong transcription	Dnd41	blood
16	chr10:98979600-98990000	Strong transcription	Thymus	Thymus
17	chr10:98979600-99003400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr10:98980200-98989600	Strong transcription	Primary T cells from cord blood	blood
19	chr10:98980200-98992800	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr10:98980600-98990400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr10:98980800-98988800	Weak transcription	A549	lung
22	chr10:98981000-99018200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr10:98981400-98989200	Strong transcription	Fetal Muscle Leg	muscle
24	chr10:98981400-98989600	Strong transcription	Primary hematopoietic stem cells	blood
25	chr10:98981400-98990400	Strong transcription	Fetal Muscle Trunk	muscle
26	chr10:98981400-99025400	Weak transcription	Colon Smooth Muscle	Colon
27	chr10:98982200-98988800	Strong transcription	Lung	lung
28	chr10:98982200-98990000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr10:98982200-98990200	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr10:98982200-98991600	Strong transcription	Primary B cells from cord blood	blood
31	chr10:98982400-98988600	Weak transcription	Fetal Kidney	kidney
32	chr10:98982400-98998800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr10:98982400-99003400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr10:98982600-98992000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr10:98982600-98993200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr10:98982600-99007600	Weak transcription	Fetal Brain Female	brain
37	chr10:98982600-99007600	Weak transcription	Placenta	Placenta
38	chr10:98982600-99020800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr10:98982800-98999200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr10:98983000-98994200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr10:98983000-99003400	Weak transcription	Brain Anterior Caudate	brain
42	chr10:98983000-99022000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr10:98983000-99027200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr10:98983000-99027400	Weak transcription	Psoas Muscle	Psoas
45	chr10:98983000-99037600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr10:98983200-98990200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr10:98983200-98994600	Weak transcription	Ovary	ovary
48	chr10:98983200-99027400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr10:98983800-98992600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr10:98984400-98989600	Strong transcription	Sigmoid Colon	Sigmoid Colon

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