Variant report

Variant	rs17668731
Chromosome Location	chr4:87999483-87999484
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87997558..88001299-chr4:88002036..88005142,4	K562	blood:
2	chr4:87926924..87928718-chr4:87999018..88000615,2	MCF-7	breast:
3	chr4:87926823..87929290-chr4:87998316..87999990,2	K562	blood:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10003331	1.00[ASN][1000 genomes]
rs10015544	1.00[ASN][1000 genomes]
rs10022825	1.00[ASN][1000 genomes]
rs10032200	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10050309	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1037813	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489044	1.00[ASW][hapmap];0.91[MEX][hapmap]
rs12508231	1.00[ASN][1000 genomes]
rs12646299	1.00[YRI][hapmap]
rs13103234	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13108043	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13134084	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17012304	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17030453	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17604937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17668952	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17703261	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2230858	1.00[ASN][1000 genomes]
rs28495374	1.00[ASN][1000 genomes]
rs28667805	1.00[ASN][1000 genomes]
rs28791499	1.00[ASN][1000 genomes]
rs35658582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35849753	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs366327	1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41525049	0.91[MEX][hapmap]
rs431836	1.00[ASW][hapmap];0.91[MEX][hapmap]
rs4693158	1.00[YRI][hapmap]
rs56656813	1.00[ASN][1000 genomes]
rs57954253	1.00[ASN][1000 genomes]
rs58478399	1.00[ASN][1000 genomes]
rs59526367	1.00[ASN][1000 genomes]
rs62306540	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817981	1.00[ASN][1000 genomes]
rs6822384	1.00[ASN][1000 genomes]
rs6846149	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6846352	1.00[ASN][1000 genomes]
rs71607404	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72877916	1.00[ASN][1000 genomes]
rs72877918	1.00[ASN][1000 genomes]
rs73839171	1.00[ASN][1000 genomes]
rs7664479	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7668285	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs967552	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv879525	chr4:87964363-88033352	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17668731	AFF1	cis	cerebellum	SCAN
rs17668731	DMP1	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87982600-87999600	Weak transcription	K562	blood
2	chr4:87990200-87999600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:87990200-88008000	Weak transcription	Spleen	Spleen
4	chr4:87990800-88000200	Weak transcription	Fetal Brain Female	brain
5	chr4:87995200-87999600	Weak transcription	Fetal Muscle Leg	muscle
6	chr4:87995200-88000000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:87995200-88000200	Weak transcription	NH-A	brain
8	chr4:87995200-88000800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr4:87995200-88009400	Weak transcription	HepG2	liver
10	chr4:87995200-88010600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr4:87995200-88029200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:87995400-87999800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr4:87995400-88000000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:87995400-88006200	Weak transcription	Hela-S3	cervix
15	chr4:87995400-88037800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:87995600-88000000	Weak transcription	Stomach Mucosa	stomach
17	chr4:87995600-88000200	Weak transcription	Fetal Kidney	kidney
18	chr4:87995600-88000400	Weak transcription	Fetal Thymus	thymus
19	chr4:87995600-88001000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr4:87995600-88001000	Weak transcription	Thymus	Thymus
21	chr4:87995600-88001200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr4:87995600-88001200	Weak transcription	Esophagus	oesophagus
23	chr4:87995600-88001400	Weak transcription	Fetal Intestine Small	intestine
24	chr4:87995600-88001600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr4:87995600-88005200	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr4:87995600-88011200	Weak transcription	Colonic Mucosa	Colon
27	chr4:87995800-88000200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:87995800-88003000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr4:87995800-88005200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:87995800-88005200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr4:87995800-88023800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr4:87996000-88005400	Weak transcription	Primary T cells from cord blood	blood
33	chr4:87996000-88005400	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr4:87996000-88005800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr4:87996200-87999800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr4:87996200-88000400	Weak transcription	Dnd41	blood
37	chr4:87996200-88000600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr4:87996200-88005200	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr4:87996400-88005000	Weak transcription	Primary B cells from cord blood	blood
40	chr4:87996600-87999600	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr4:87996800-87999600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:87996800-88000600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr4:87996800-88004400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr4:87996800-88023600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr4:87997200-88000200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:87997200-88000200	Enhancers	NHEK	skin
47	chr4:87997400-87999600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr4:87997600-87999600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:87997600-88000200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr4:87997800-87999600	Enhancers	Skeletal Muscle Female	skeletal muscle

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