Variant report

Variant	rs17622920
Chromosome Location	chr10:18951085-18951086
allele	A/G
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	IRF1	chr10:18950275-18951108	K562	blood:	n/a	chr10:18950399-18950408 chr10:18950981-18950994
2	POLR2A	chr10:18950575-18951332	A549	lung:	n/a	n/a
3	POLR2A	chr10:18950074-18951237	K562	blood:	n/a	n/a
4	CHD1	chr10:18946884-18951792	IMR90	lung:	n/a	chr10:18948546-18948556 chr10:18948735-18948745
5	POLR2A	chr10:18949923-18951350	HepG2	liver:	n/a	n/a
6	POLR2A	chr10:18946803-18951639	IMR90	lung:	n/a	n/a
7	POLR2A	chr10:18950108-18951270	GM12878	blood:	n/a	n/a
8	POLR2A	chr10:18950080-18951470	HepG2	liver:	n/a	n/a
9	WRNIP1	chr10:18950714-18951210	GM12878	blood:	n/a	n/a
10	POLR2A	chr10:18951008-18951292	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:18909074..18910706-chr10:18949247..18951149,2	K562	blood:
2	chr10:18937279..18942257-chr10:18944156..18951752,16	MCF-7	breast:

Variant related genes	Relation type
ARL5B-AS1	TF binding region
ENSG00000241058	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10764566	1.00[JPT][hapmap]
rs10764584	1.00[JPT][hapmap]
rs10828835	1.00[JPT][hapmap]
rs10828859	1.00[JPT][hapmap]
rs10828879	1.00[JPT][hapmap]
rs10828906	1.00[JPT][hapmap]
rs11015307	1.00[JPT][hapmap]
rs11015416	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11015454	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12357594	0.93[EUR][1000 genomes]
rs12359572	0.81[EUR][1000 genomes]
rs12772534	1.00[JPT][hapmap]
rs1352655	1.00[JPT][hapmap]
rs17623007	1.00[ASN][1000 genomes]
rs17695669	0.95[CEU][hapmap]
rs1971272	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2035752	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34503140	1.00[ASN][1000 genomes]
rs4279920	1.00[ASN][1000 genomes]
rs45580334	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4578284	1.00[JPT][hapmap]
rs4747353	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4748480	1.00[JPT][hapmap]
rs4748495	1.00[JPT][hapmap]
rs61298471	1.00[ASN][1000 genomes]
rs6482516	1.00[JPT][hapmap]
rs6482529	1.00[JPT][hapmap]
rs7073751	1.00[ASN][1000 genomes]
rs7081811	1.00[JPT][hapmap]
rs7088214	1.00[JPT][hapmap]
rs7093518	1.00[ASN][1000 genomes]
rs7095070	1.00[JPT][hapmap]
rs7098313	1.00[JPT][hapmap]
rs7098826	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7099975	1.00[JPT][hapmap]
rs7902450	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7905730	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7917217	1.00[ASN][1000 genomes]
rs7917323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers 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 target site	16 gene(s)	inside rSNPs	diseases
2	nsv466762	chr10:18932172-18976659	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv550121	chr10:18932172-18976659	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17622920	NSUN6	cis	lung	GTEx
rs17622920	CACNB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18947000-18951200	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr10:18947400-18951600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr10:18948800-18951200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr10:18949000-18954000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr10:18949400-18951200	Enhancers	Brain Substantia Nigra	brain
6	chr10:18949400-18951400	Flanking Active TSS	Dnd41	blood
7	chr10:18949400-18973200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr10:18949600-18951200	Enhancers	Gastric	stomach
9	chr10:18949600-18951200	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr10:18949600-18951400	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr10:18949600-18951400	Enhancers	Brain Hippocampus Middle	brain
12	chr10:18949600-18951400	Enhancers	Colon Smooth Muscle	Colon
13	chr10:18949600-18951400	Enhancers	Fetal Brain Male	brain
14	chr10:18949600-18951600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr10:18949600-18951800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr10:18949600-18952400	Enhancers	Primary T cells fromperipheralblood	blood
17	chr10:18949600-18952400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr10:18949600-18953800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr10:18949600-18957000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr10:18949600-18972000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr10:18949800-18951200	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr10:18949800-18951400	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr10:18949800-18951600	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr10:18949800-18952200	Enhancers	Small Intestine	intestine
25	chr10:18949800-18956600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr10:18950000-18951200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr10:18950000-18951200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr10:18950000-18951200	Enhancers	Fetal Thymus	thymus
29	chr10:18950000-18951200	Enhancers	Pancreas	Pancrea
30	chr10:18950000-18953800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr10:18950000-18956600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr10:18950000-18957600	Weak transcription	Fetal Stomach	stomach
33	chr10:18950200-18951200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr10:18950200-18951200	Enhancers	Right Atrium	heart
35	chr10:18950200-18951200	Enhancers	HMEC	breast
36	chr10:18950200-18951200	Enhancers	HUVEC	blood vessel
37	chr10:18950200-18951400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr10:18950200-18951400	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr10:18950200-18953600	Weak transcription	Lung	lung
40	chr10:18950200-18954600	Weak transcription	HSMM	muscle
41	chr10:18950200-18956000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr10:18950200-18956800	Weak transcription	Left Ventricle	heart
43	chr10:18950200-18957000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr10:18950200-18957000	Weak transcription	Fetal Muscle Trunk	muscle
45	chr10:18950200-18957600	Weak transcription	Placenta	Placenta
46	chr10:18950400-18951200	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr10:18950400-18951200	Enhancers	Primary hematopoietic stem cells	blood
48	chr10:18950400-18951200	Flanking Active TSS	Brain Angular Gyrus	brain
49	chr10:18950400-18951400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr10:18950400-18951400	Weak transcription	HSMMtube	muscle

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