Variant report

Variant	rs363098
Chromosome Location	chr4:3174256-3174257
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3173185..3175409-chr4:3176697..3178512,2	MCF-7	breast:
2	chr4:3174198..3176315-chr4:3186979..3189663,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10006373	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10012793	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021254	1.00[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs10034669	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10155264	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10488840	1.00[EUR][1000 genomes]
rs16844026	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16844028	1.00[EUR][1000 genomes]
rs2003530	0.97[EUR][1000 genomes]
rs2005787	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28436280	0.92[EUR][1000 genomes]
rs28507598	0.83[EUR][1000 genomes]
rs28643391	0.99[EUR][1000 genomes]
rs28834148	1.00[ASN][1000 genomes]
rs3025825	0.99[EUR][1000 genomes]
rs362269	0.82[EUR][1000 genomes]
rs362274	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs362276	0.91[EUR][1000 genomes]
rs362278	1.00[EUR][1000 genomes]
rs362303	0.85[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs362305	0.80[EUR][1000 genomes]
rs362310	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs362323	0.99[EUR][1000 genomes]
rs362325	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs362338	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs363067	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs363068	1.00[ASN][1000 genomes]
rs363070	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs363082	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs363090	0.93[EUR][1000 genomes]
rs363091	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs363093	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363094	0.97[EUR][1000 genomes]
rs363095	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs363097	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363100	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363101	0.95[EUR][1000 genomes]
rs363106	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs363124	0.93[EUR][1000 genomes]
rs363125	0.93[EUR][1000 genomes]
rs363128	1.00[EUR][1000 genomes]
rs363141	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59147561	1.00[ASN][1000 genomes]
rs59588638	0.85[EUR][1000 genomes]
rs61792464	1.00[ASN][1000 genomes]
rs61792535	0.87[EUR][1000 genomes]
rs6446724	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446725	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828615	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828882	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829069	1.00[CHD][hapmap]
rs6834455	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835567	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839081	0.93[EUR][1000 genomes]
rs6839274	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843895	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7438553	0.96[EUR][1000 genomes]
rs7654034	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7663133	1.00[ASN][1000 genomes]
rs7665816	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7667354	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682324	1.00[ASN][1000 genomes]
rs7683309	1.00[EUR][1000 genomes]
rs7688390	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9993542	1.00[CHD][hapmap]
rs9993781	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs363098	OTOP1	cis	cerebellum	SCAN
rs363098	SH3BP2	cis	cerebellum	SCAN
rs363098	TMEM129	cis	parietal	SCAN
rs363098	JAKMIP1	cis	cerebellum	SCAN

Chromatin state (count:127 , 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	chr4:3150000-3174400	Weak transcription	HMEC	breast
4	chr4:3162400-3174600	Weak transcription	HUVEC	blood vessel
5	chr4:3162400-3175000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr4:3162600-3182200	Weak transcription	Small Intestine	intestine
7	chr4:3163000-3182000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:3164200-3174400	Weak transcription	Fetal Brain Male	brain
9	chr4:3164600-3174800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr4:3166200-3177400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:3167800-3203400	Strong transcription	Primary B cells from peripheral blood	blood
12	chr4:3168000-3180800	Strong transcription	Fetal Stomach	stomach
13	chr4:3168000-3182600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:3168000-3191800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr4:3168000-3192600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr4:3168000-3197600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:3168000-3202800	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr4:3168000-3203000	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr4:3170000-3208800	Weak transcription	Stomach Mucosa	stomach
20	chr4:3170200-3174800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr4:3170200-3181200	Weak transcription	K562	blood
22	chr4:3170200-3185000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr4:3170600-3174400	Weak transcription	Fetal Heart	heart
24	chr4:3170600-3182200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr4:3171200-3186600	Strong transcription	GM12878-XiMat	blood
26	chr4:3171200-3197600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:3171400-3178000	Strong transcription	Fetal Muscle Trunk	muscle
28	chr4:3171400-3187200	Strong transcription	Primary B cells from cord blood	blood
29	chr4:3171400-3192800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr4:3171600-3178200	Strong transcription	Fetal Muscle Leg	muscle
31	chr4:3171600-3192800	Strong transcription	Primary T cells from cord blood	blood
32	chr4:3171600-3193600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr4:3171800-3180800	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr4:3172000-3180000	Strong transcription	HepG2	liver
35	chr4:3172000-3192000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr4:3172000-3202800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr4:3172200-3178000	Strong transcription	Fetal Intestine Small	intestine
38	chr4:3172200-3180400	Strong transcription	Liver	Liver
39	chr4:3172200-3193000	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr4:3172200-3195400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr4:3172400-3199800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:3172400-3238800	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr4:3172600-3192400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr4:3172800-3202800	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr4:3173000-3181200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr4:3173000-3192600	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr4:3173000-3193000	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr4:3173200-3182600	Strong transcription	Dnd41	blood
49	chr4:3173400-3175600	Strong transcription	Primary hematopoietic stem cells	blood
50	chr4:3173400-3177000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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