Variant report

Variant	rs2540168
Chromosome Location	chr1:156223823-156223824
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	POLR2A	chr1:156223669-156223880	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:156223433-156224113	GM12891	blood:	n/a	n/a
3	POLR2A	chr1:156223386-156224028	K562	blood:	n/a	n/a
4	POLR2A	chr1:156223201-156224195	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:156223381-156224152	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr1:156223438-156223876	K562	blood:	n/a	n/a
7	POLR2A	chr1:156223761-156224084	GM12892	blood:	n/a	n/a
8	POLR2A	chr1:156223620-156223862	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:156223608-156224124	K562	blood:	n/a	n/a
10	POLR2A	chr1:156223358-156224095	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:156217088..156223481-chr1:156223797..156227498,6	K562	blood:
2	chr1:156219284..156221602-chr1:156221883..156224830,2	MCF-7	breast:

Variant related genes	Relation type
SMG5	TF binding region
ENSG00000198952	Chromatin interaction
ENSG00000160781	Chromatin interaction

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

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

rs_ID	r²[population]
rs1800247	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2246476	0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.93[ASN][1000 genomes]
rs2253358	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]
rs2495269	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap]
rs2540169	0.91[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2764406	0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.83[YRI][hapmap]
rs2764407	0.95[CHB][hapmap];0.83[YRI][hapmap]
rs2985711	0.82[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	nsv872470	chr1:156210557-156223823	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2540168	PAQR6	cis	Whole Blood	GTEx
rs2540168	SMG5	cis	Whole Blood	GTEx
rs2540168	TCHHL1	cis	cerebellum	SCAN
rs2540168	SPRR2A	cis	parietal	SCAN
rs2540168	C1orf85	cis	Whole Blood	GTEx
rs2540168	FAM189B	cis	cerebellum	SCAN
rs2540168	APOA1BP	cis	cerebellum	SCAN
rs2540168	ADAM15	cis	cerebellum	SCAN
rs2540168	SPRR2B	cis	cerebellum	SCAN
rs2540168	C1orf61	cis	cerebellum	SCAN
rs2540168	PAQR6	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 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	chr1:156216400-156224600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr1:156217400-156245200	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:156217800-156229600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:156217800-156249000	Strong transcription	Thymus	Thymus
7	chr1:156217800-156250400	Strong transcription	Fetal Intestine Small	intestine
8	chr1:156218000-156224200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:156218000-156249000	Strong transcription	Spleen	Spleen
10	chr1:156218200-156230000	Weak transcription	Fetal Brain Male	brain
11	chr1:156218200-156250000	Weak transcription	Right Atrium	heart
12	chr1:156218200-156250400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:156218200-156250400	Strong transcription	Fetal Stomach	stomach
14	chr1:156218400-156232400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:156218600-156224000	Strong transcription	Rectal Smooth Muscle	rectum
16	chr1:156218600-156224400	Strong transcription	Gastric	stomach
17	chr1:156218600-156224600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:156218600-156246800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:156218600-156250400	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:156218800-156224000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:156218800-156224000	Strong transcription	Esophagus	oesophagus
22	chr1:156218800-156224200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:156218800-156224200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr1:156218800-156224200	Strong transcription	Fetal Brain Female	brain
25	chr1:156218800-156224200	Strong transcription	HSMM	muscle
26	chr1:156218800-156224400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr1:156218800-156224400	Strong transcription	NHLF	lung
28	chr1:156218800-156224600	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr1:156218800-156224600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:156218800-156224600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:156218800-156224600	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:156218800-156224800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:156218800-156227200	Strong transcription	Primary T cells from cord blood	blood
34	chr1:156218800-156227400	Strong transcription	Placenta	Placenta
35	chr1:156218800-156227600	Strong transcription	Fetal Muscle Leg	muscle
36	chr1:156218800-156230000	Strong transcription	Liver	Liver
37	chr1:156218800-156232200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:156218800-156245000	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr1:156218800-156245600	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr1:156218800-156249000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:156218800-156249200	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr1:156218800-156250200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:156218800-156250200	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:156218800-156250400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:156218800-156250400	Strong transcription	Fetal Intestine Large	intestine
46	chr1:156219000-156224200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:156219000-156224200	Strong transcription	Colon Smooth Muscle	Colon
48	chr1:156219000-156224200	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:156219000-156224800	Strong transcription	Brain Germinal Matrix	brain
50	chr1:156219000-156227200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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