Variant report

Variant	rs1557474
Chromosome Location	chr11:75185648-75185649
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:75185179..75187092-chr11:75248204..75250033,2	K562	blood:
2	chr11:75177141..75179157-chr11:75184884..75186837,2	K562	blood:
3	chr11:75185137..75187494-chr11:75526962..75529134,2	K562	blood:
4	chr11:75184064..75186099-chr11:75244472..75246360,2	K562	blood:
5	chr11:75184591..75187071-chr11:75200307..75202910,2	MCF-7	breast:
6	chr11:75182448..75185750-chr11:75189999..75193273,3	K562	blood:

Variant related genes	Relation type
ENSG00000158555	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1004856	0.89[YRI][hapmap];0.89[AFR][1000 genomes]
rs10751243	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1557471	0.89[YRI][hapmap]
rs1623440	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1631470	0.93[YRI][hapmap]
rs1631865	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1790145	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1790149	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790153	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790154	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1790155	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1790156	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790158	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1790160	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1793398	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs1793411	0.88[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1793412	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1793414	0.93[YRI][hapmap];0.90[AFR][1000 genomes]
rs1793415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894213	1.00[CHB][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs471857	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs473462	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs474056	0.92[CHB][hapmap];0.87[EUR][1000 genomes]
rs482458	1.00[CHB][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs482503	1.00[CHB][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs486326	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs488305	0.92[CHB][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs492309	0.86[EUR][1000 genomes]
rs504685	1.00[CHB][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs518611	1.00[CHB][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs523617	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs532454	1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs535520	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs535523	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs546632	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs547844	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs550957	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs609793	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs611449	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs623338	1.00[CEU][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs625938	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs628972	0.83[ASW][hapmap];0.87[LWK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs653673	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs668727	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[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	esv3381903	chr11:75123498-75587233	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv897923	chr11:75129007-75302855	Active TSS Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	esv993847	chr11:75176894-75187181	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1557474	ARAP1	cis	cerebellum	SCAN
rs1557474	IL18BP	cis	parietal	SCAN
rs1557474	PLEKHB1	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75144200-75186600	Weak transcription	Gastric	stomach
2	chr11:75145200-75186200	Weak transcription	Primary T cells from cord blood	blood
3	chr11:75145200-75186400	Strong transcription	Fetal Intestine Small	intestine
4	chr11:75147800-75186000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr11:75148200-75186000	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr11:75163800-75186200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr11:75165200-75187000	Strong transcription	HepG2	liver
8	chr11:75166600-75186800	Weak transcription	Pancreas	Pancrea
9	chr11:75173600-75185800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr11:75174600-75186600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr11:75177400-75186800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:75178600-75185800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr11:75180200-75186000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr11:75180200-75186600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr11:75180400-75186000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr11:75180400-75186400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr11:75180400-75186400	Weak transcription	Brain Germinal Matrix	brain
18	chr11:75180400-75186400	Weak transcription	Colon Smooth Muscle	Colon
19	chr11:75180400-75186400	Weak transcription	Osteobl	bone
20	chr11:75180600-75185800	Weak transcription	K562	blood
21	chr11:75180600-75186400	Weak transcription	Right Atrium	heart
22	chr11:75181600-75186400	Genic enhancers	Placenta	Placenta
23	chr11:75181800-75188800	Enhancers	Fetal Muscle Trunk	muscle
24	chr11:75182400-75192400	Strong transcription	Fetal Intestine Large	intestine
25	chr11:75182600-75187200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr11:75183600-75186400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr11:75183800-75186200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr11:75183800-75186400	Weak transcription	HSMM	muscle
29	chr11:75183800-75187000	Weak transcription	NHEK	skin
30	chr11:75184000-75186600	Weak transcription	Fetal Brain Female	brain
31	chr11:75184000-75186800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr11:75184200-75187800	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr11:75184400-75185800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr11:75184400-75186400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:75184400-75186400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
36	chr11:75184400-75187000	Enhancers	Fetal Stomach	stomach
37	chr11:75184400-75188800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr11:75184600-75186400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr11:75184600-75186600	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr11:75184600-75187400	Weak transcription	HSMMtube	muscle
41	chr11:75184600-75188400	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr11:75184600-75188400	Enhancers	Fetal Thymus	thymus
43	chr11:75184800-75186400	Weak transcription	Fetal Brain Male	brain
44	chr11:75184800-75187400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:75184800-75188800	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr11:75185000-75186400	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr11:75185000-75186600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr11:75185000-75187800	Enhancers	HUVEC	blood vessel
49	chr11:75185000-75189000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr11:75185200-75186200	Enhancers	Monocytes-CD14+_RO01746	blood

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