Variant report

Variant	rs2253358
Chromosome Location	chr1:156228060-156228061
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr1:156226813-156228334	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr1:156227959-156228401	PFSK-1	brain:	n/a	n/a
3	EP300	chr1:156226339-156228367	SK-N-SH	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:156227270..156229254-chr1:156230884..156233634,2	K562	blood:
2	chr1:156226246..156228818-chr1:156235948..156239985,3	K562	blood:
3	chr1:156227645..156230794-chr1:156250788..156253633,3	MCF-7	breast:
4	chr1:156226382..156228155-chr1:156230487..156233369,2	MCF-7	breast:
5	chr1:156225781..156228623-chr1:156250974..156252737,2	K562	blood:
6	chr1:156227464..156230877-chr1:156233659..156236804,3	MCF-7	breast:

No data

Variant related genes	Relation type
SMG5	TF binding region
ENSG00000163472	Chromatin interaction
ENSG00000198952	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1800247	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2246476	0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2495269	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap]
rs2540168	0.91[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2540169	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2764406	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.83[YRI][hapmap]
rs2764407	0.89[CEU][hapmap];0.95[CHB][hapmap];0.83[YRI][hapmap]
rs2985711	0.94[CEU][hapmap];0.90[CHB][hapmap]

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	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases
2	nsv1011302	chr1:156081561-156532624	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	380 gene(s)	inside rSNPs	diseases
3	nsv915822	chr1:156226286-156651655	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	367 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2253358	MGC13102	cis	multi-tissue	Pritchard
rs2253358	ADAM15	cis	cerebellum	SCAN
rs2253358	C1orf85	cis	Whole Blood	GTEx
rs2253358	TCHHL1	cis	cerebellum	SCAN
rs2253358	APOA1BP	cis	cerebellum	SCAN
rs2253358	PAQR6	cis	Whole Blood	GTEx
rs2253358	EST1B	cis	multi-tissue	Pritchard
rs2253358	SMG5	cis	Whole Blood	GTEx
rs2253358	FAM189B	cis	cerebellum	SCAN
rs2253358	SPRR2B	cis	cerebellum	SCAN
rs2253358	C1orf61	cis	cerebellum	SCAN
rs2253358	C1orf85	cis	multi-tissue	Pritchard
rs2253358	PAQR6	cis	lymphoblastoid	seeQTL
rs2253358	PAQR6	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:156211600-156251600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:156214400-156233000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:156217400-156245200	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr1:156217800-156229600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:156217800-156249000	Strong transcription	Thymus	Thymus
6	chr1:156217800-156250400	Strong transcription	Fetal Intestine Small	intestine
7	chr1:156218000-156249000	Strong transcription	Spleen	Spleen
8	chr1:156218200-156230000	Weak transcription	Fetal Brain Male	brain
9	chr1:156218200-156250000	Weak transcription	Right Atrium	heart
10	chr1:156218200-156250400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:156218200-156250400	Strong transcription	Fetal Stomach	stomach
12	chr1:156218400-156232400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:156218600-156246800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:156218600-156250400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:156218800-156230000	Strong transcription	Liver	Liver
16	chr1:156218800-156232200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:156218800-156245000	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr1:156218800-156245600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr1:156218800-156249000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:156218800-156249200	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr1:156218800-156250200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:156218800-156250200	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:156218800-156250400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:156218800-156250400	Strong transcription	Fetal Intestine Large	intestine
25	chr1:156219000-156249800	Strong transcription	Dnd41	blood
26	chr1:156219000-156250400	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:156219200-156230600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:156219200-156239000	Strong transcription	Colonic Mucosa	Colon
29	chr1:156219200-156239000	Strong transcription	Stomach Smooth Muscle	stomach
30	chr1:156219200-156249200	Strong transcription	Lung	lung
31	chr1:156219200-156249600	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:156219200-156250000	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr1:156219200-156250200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:156219200-156250600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr1:156219400-156249600	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr1:156219400-156250400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr1:156220000-156232200	Strong transcription	Osteobl	bone
38	chr1:156220000-156250200	Strong transcription	Primary B cells from peripheral blood	blood
39	chr1:156221000-156250400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr1:156222000-156232600	Strong transcription	Left Ventricle	heart
41	chr1:156222000-156250000	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:156222400-156248800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:156222400-156249200	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:156222400-156249400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:156222400-156250000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr1:156222600-156228400	Weak transcription	Stomach Mucosa	stomach
47	chr1:156222800-156233400	Strong transcription	Right Ventricle	heart
48	chr1:156222800-156247800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:156223800-156229000	Weak transcription	Small Intestine	intestine
50	chr1:156224000-156229800	Weak transcription	Psoas Muscle	Psoas

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