Variant report

Variant	rs10488840
Chromosome Location	chr4:3186993-3186994
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3174198..3176315-chr4:3186979..3189663,2	K562	blood:
2	chr4:3186114..3188312-chr4:3216098..3217780,2	MCF-7	breast:
3	chr4:3110166..3112749-chr4:3184867..3187670,2	MCF-7	breast:

Extended variants
information (count: 103 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10006373	0.93[EUR][1000 genomes]
rs10012793	0.81[EUR][1000 genomes]
rs10021254	0.92[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10034669	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10155264	0.92[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1065745	1.00[ASN][1000 genomes]
rs16843803	1.00[ASN][1000 genomes]
rs16844026	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16844028	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17780617	1.00[ASN][1000 genomes]
rs2003530	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2005787	0.95[EUR][1000 genomes]
rs28436280	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28507598	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28643391	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3025825	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34045730	1.00[ASN][1000 genomes]
rs34591077	1.00[ASN][1000 genomes]
rs362269	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs362274	0.89[CEU][hapmap];0.96[EUR][1000 genomes]
rs362276	0.91[EUR][1000 genomes]
rs362278	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs362303	0.86[GIH][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs362304	1.00[ASN][1000 genomes]
rs362305	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs362310	0.92[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs362323	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs362325	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs362338	0.92[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];1.00[EUR][1000 genomes]
rs363065	1.00[ASN][1000 genomes]
rs363069	1.00[ASN][1000 genomes]
rs363071	1.00[ASN][1000 genomes]
rs363078	1.00[ASN][1000 genomes]
rs363084	1.00[ASN][1000 genomes]
rs363087	1.00[ASN][1000 genomes]
rs363089	1.00[ASN][1000 genomes]
rs363090	0.93[EUR][1000 genomes]
rs363091	0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs363093	0.93[EUR][1000 genomes]
rs363094	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363095	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363097	0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs363098	1.00[EUR][1000 genomes]
rs363100	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[EUR][1000 genomes]
rs363101	0.95[EUR][1000 genomes]
rs363103	1.00[ASN][1000 genomes]
rs363105	1.00[ASN][1000 genomes]
rs363106	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs363124	0.93[EUR][1000 genomes]
rs363125	0.93[EUR][1000 genomes]
rs363128	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363141	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs56794194	1.00[ASN][1000 genomes]
rs57196404	1.00[ASN][1000 genomes]
rs59588638	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61460614	1.00[ASN][1000 genomes]
rs61583241	1.00[ASN][1000 genomes]
rs61790489	1.00[ASN][1000 genomes]
rs61790490	1.00[ASN][1000 genomes]
rs61792472	1.00[ASN][1000 genomes]
rs61792477	1.00[ASN][1000 genomes]
rs61792500	1.00[ASN][1000 genomes]
rs61792501	1.00[ASN][1000 genomes]
rs61792502	1.00[ASN][1000 genomes]
rs61792503	1.00[ASN][1000 genomes]
rs61792505	1.00[ASN][1000 genomes]
rs61792507	1.00[ASN][1000 genomes]
rs61792508	1.00[ASN][1000 genomes]
rs61792509	1.00[ASN][1000 genomes]
rs61792510	1.00[ASN][1000 genomes]
rs61792512	1.00[ASN][1000 genomes]
rs61792515	1.00[ASN][1000 genomes]
rs61792531	1.00[ASN][1000 genomes]
rs61792532	1.00[ASN][1000 genomes]
rs61792533	1.00[ASN][1000 genomes]
rs61792535	0.87[EUR][1000 genomes]
rs6446724	1.00[EUR][1000 genomes]
rs6446725	1.00[EUR][1000 genomes]
rs6828615	0.88[EUR][1000 genomes]
rs6828882	0.99[EUR][1000 genomes]
rs6834455	0.92[CEU][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs6835567	0.92[EUR][1000 genomes]
rs6839081	0.93[EUR][1000 genomes]
rs6839274	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[EUR][1000 genomes]
rs6843895	0.92[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs73073018	1.00[ASN][1000 genomes]
rs7438553	0.96[EUR][1000 genomes]
rs7654034	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs7665816	0.92[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs7667354	1.00[EUR][1000 genomes]
rs7674122	1.00[ASN][1000 genomes]
rs7683309	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686771	1.00[ASN][1000 genomes]
rs7688390	0.85[EUR][1000 genomes]
rs7699037	1.00[ASN][1000 genomes]
rs9993781	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	nsv461164	chr4:3149016-3215835	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv593439	chr4:3149016-3215835	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10488840	SH3BP2	cis	cerebellum	SCAN
rs10488840	TMEM129	cis	parietal	SCAN
rs10488840	JAKMIP1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3114600-3292400	Weak transcription	Right Atrium	heart
2	chr4:3145800-3239200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:3167800-3203400	Strong transcription	Primary B cells from peripheral blood	blood
4	chr4:3168000-3191800	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr4:3168000-3192600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:3168000-3197600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr4:3168000-3202800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr4:3168000-3203000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr4:3170000-3208800	Weak transcription	Stomach Mucosa	stomach
10	chr4:3171200-3197600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:3171400-3187200	Strong transcription	Primary B cells from cord blood	blood
12	chr4:3171400-3192800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr4:3171600-3192800	Strong transcription	Primary T cells from cord blood	blood
14	chr4:3171600-3193600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:3172000-3192000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr4:3172000-3202800	Strong transcription	Duodenum Mucosa	Duodenum
17	chr4:3172200-3193000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr4:3172200-3195400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr4:3172400-3199800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:3172400-3238800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:3172600-3192400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr4:3172800-3202800	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr4:3173000-3192600	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr4:3173000-3193000	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr4:3173400-3188800	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:3173600-3187000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:3173600-3188000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:3173600-3192800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:3173600-3192800	Strong transcription	Placenta	Placenta
30	chr4:3173600-3193000	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr4:3173600-3200000	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr4:3173800-3192800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:3173800-3192800	Strong transcription	Fetal Thymus	thymus
34	chr4:3173800-3193400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:3174000-3192600	Strong transcription	Thymus	Thymus
36	chr4:3174000-3192600	Strong transcription	Spleen	Spleen
37	chr4:3174000-3192800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr4:3174000-3192800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:3174000-3204000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr4:3176400-3199600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:3177000-3189600	Weak transcription	Fetal Heart	heart
42	chr4:3177000-3189800	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr4:3177600-3189600	Weak transcription	Psoas Muscle	Psoas
44	chr4:3177800-3192600	Strong transcription	Left Ventricle	heart
45	chr4:3178400-3195200	Strong transcription	Fetal Muscle Trunk	muscle
46	chr4:3178800-3200000	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr4:3179400-3192400	Strong transcription	Adipose Nuclei	Adipose
48	chr4:3179400-3192800	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr4:3179600-3188000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr4:3179600-3188600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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