Variant report

Variant	rs2798221
Chromosome Location	chr4:3270488-3270489
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3268743..3271551-chr4:3273568..3275857,3	MCF-7	breast:
2	chr4:3265031..3267765-chr4:3268616..3271432,2	K562	blood:
3	chr4:3243269..3245646-chr4:3270348..3272217,2	MCF-7	breast:
4	chr4:3269730..3272201-chr4:3294200..3296416,2	MCF-7	breast:
5	chr4:3269278..3270856-chr4:3292386..3294072,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1006798	0.82[ASN][1000 genomes]
rs10155132	0.80[CHB][hapmap]
rs10805008	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs108850	0.90[JPT][hapmap]
rs10937921	0.84[ASN][1000 genomes]
rs110501	0.90[JPT][hapmap]
rs2071667	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071668	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2108753	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2157090	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2157091	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2157092	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2236052	0.90[CHB][hapmap]
rs2239725	0.89[CHB][hapmap]
rs2530597	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2530599	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2530601	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2749781	0.85[CHB][hapmap]
rs2749782	0.85[CHB][hapmap]
rs2749785	0.90[CHB][hapmap]
rs2798222	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2798224	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2798225	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2858083	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2858084	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2858085	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2858086	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2858087	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2858088	0.95[ASN][1000 genomes]
rs3095072	0.86[ASN][1000 genomes]
rs3095073	0.86[ASN][1000 genomes]
rs3095074	0.83[ASN][1000 genomes]
rs3095077	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3095079	0.97[ASN][1000 genomes]
rs3095080	0.91[ASN][1000 genomes]
rs3095081	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs3095082	0.86[ASN][1000 genomes]
rs3095083	0.86[ASN][1000 genomes]
rs3121420	0.95[ASN][1000 genomes]
rs3129308	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs3129310	0.80[CHB][hapmap]
rs3129319	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3129320	0.94[ASN][1000 genomes]
rs3129327	0.84[CHB][hapmap]
rs3129328	0.85[CHB][hapmap]
rs3135064	0.83[ASN][1000 genomes]
rs3135145	0.84[CHB][hapmap]
rs3135146	0.90[CHB][hapmap]
rs3135168	0.93[ASN][1000 genomes]
rs3135169	0.84[ASN][1000 genomes]
rs3135170	0.83[ASN][1000 genomes]
rs3135171	0.83[ASN][1000 genomes]
rs362266	0.82[ASN][1000 genomes]
rs362273	0.85[JPT][hapmap]
rs362279	0.83[ASN][1000 genomes]
rs362280	0.81[ASN][1000 genomes]
rs362282	0.82[ASN][1000 genomes]
rs362283	0.84[ASN][1000 genomes]
rs362296	0.85[JPT][hapmap]
rs362306	0.85[JPT][hapmap]
rs362331	0.90[JPT][hapmap]
rs363064	0.90[JPT][hapmap]
rs363066	0.85[JPT][hapmap]
rs363096	0.90[JPT][hapmap]
rs4690073	0.90[JPT][hapmap]
rs4690081	0.83[ASN][1000 genomes]
rs6446726	0.85[CEU][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6446727	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6446728	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6446731	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs6819202	0.80[CHB][hapmap]
rs6844859	0.90[JPT][hapmap]
rs6855981	0.85[JPT][hapmap]
rs7435601	0.80[CHB][hapmap]
rs7656026	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7661630	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7674472	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7675084	0.86[ASN][1000 genomes]
rs7685686	0.90[JPT][hapmap]
rs7691627	0.80[JPT][hapmap]
rs82333	0.90[JPT][hapmap]
rs881816	0.80[CHB][hapmap]
rs910568	0.81[CHB][hapmap]
rs916171	0.90[JPT][hapmap]
rs9996868	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
4	nsv524211	chr4:3215835-3270488	Strong transcription Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv470003	chr4:3215835-3275484	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv878454	chr4:3215835-3305739	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv878455	chr4:3215835-3344891	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS 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	10 gene(s)	inside rSNPs	diseases
8	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv878457	chr4:3231661-3278517	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
11	nsv878458	chr4:3235518-3303976	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
12	nsv878459	chr4:3235518-3310831	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
13	nsv878460	chr4:3260154-3303976	Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
14	nsv878461	chr4:3270488-3339038	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2798221	SH3BP2	cis	cerebellum	SCAN
rs2798221	ATP5I	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3114600-3292400	Weak transcription	Right Atrium	heart
2	chr4:3252400-3271400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:3255800-3271000	Weak transcription	Brain Hippocampus Middle	brain
4	chr4:3257000-3271800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr4:3258400-3271000	Weak transcription	Brain Anterior Caudate	brain
6	chr4:3258400-3271000	Weak transcription	Right Ventricle	heart
7	chr4:3258400-3271000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr4:3260200-3278200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr4:3264200-3273000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:3269200-3272400	Enhancers	Fetal Brain Male	brain
11	chr4:3269400-3271000	Enhancers	Placenta	Placenta
12	chr4:3269400-3271200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:3269400-3271400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr4:3269400-3271400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:3269400-3272400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr4:3269400-3272600	Enhancers	Fetal Brain Female	brain
17	chr4:3269400-3273200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:3269600-3270600	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr4:3269600-3270600	Enhancers	HMEC	breast
20	chr4:3269600-3270800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr4:3269600-3271400	Enhancers	H1 Cell Line	embryonic stem cell
22	chr4:3269600-3272400	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr4:3269600-3272800	Enhancers	Fetal Muscle Leg	muscle
24	chr4:3269800-3270600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:3269800-3272000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:3269800-3272400	Enhancers	Brain Germinal Matrix	brain
27	chr4:3270000-3271400	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr4:3270000-3274400	Weak transcription	Gastric	stomach
29	chr4:3270200-3270600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr4:3270200-3271000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:3270200-3271000	Enhancers	Pancreas	Pancrea
32	chr4:3270400-3270600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:3270400-3270600	Bivalent Enhancer	HepG2	liver
34	chr4:3270400-3271000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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