Variant report

Variant	rs16844307
Chromosome Location	chr4:3418165-3418166
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3415712..3418675-chr4:3431596..3433223,2	MCF-7	breast:
2	chr4:3402341..3405091-chr4:3416697..3418981,2	MCF-7	breast:
3	chr4:3416652..3419915-chr4:3441173..3444245,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109758	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12644442	0.90[JPT][hapmap]
rs13109976	0.89[CEU][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13116176	0.81[JPT][hapmap]
rs13127597	0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs13131192	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13152128	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1320762	0.88[CEU][hapmap];0.87[CHB][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1320763	0.89[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1406674	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs1406675	0.81[JPT][hapmap]
rs16843157	0.89[CEU][hapmap];0.80[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16844301	0.94[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16844309	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1730769	0.93[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17797467	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1894442	0.83[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs1962767	0.91[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs3025816	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs3213506	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213507	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3748036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3752442	0.81[JPT][hapmap]
rs3789739	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4690090	0.94[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes]
rs4690093	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4690095	0.82[ASN][1000 genomes]
rs4690098	0.81[JPT][hapmap]
rs58143210	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62274930	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6446740	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs6828057	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs9790656	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 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	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
4	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
5	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv878463	chr4:3363994-3498896	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv428435	chr4:3386773-3623321	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	nsv933265	chr4:3392824-4283640	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
11	esv2757918	chr4:3394344-4350986	Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Weak 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 miRNA target site	64 gene(s)	inside rSNPs	diseases
12	esv2759219	chr4:3394344-4350986	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
13	nsv461166	chr4:3405165-3451109	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv593450	chr4:3405165-3451109	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv878464	chr4:3405165-3505448	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv878465	chr4:3405165-3566567	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	esv1791851	chr4:3407753-3534022	Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
18	nsv1000383	chr4:3412585-3839781	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
19	nsv461167	chr4:3413209-3446112	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv593451	chr4:3413209-3446112	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv461168	chr4:3413209-3449652	Genic enhancers Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
22	nsv593452	chr4:3413209-3449652	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv878466	chr4:3413209-3451109	Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv878467	chr4:3413209-3454304	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers 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	3 gene(s)	inside rSNPs	diseases
25	nsv878468	chr4:3413209-3471754	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
26	nsv878469	chr4:3413209-3566567	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
27	nsv878470	chr4:3413209-3566567	Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
28	nsv878471	chr4:3413209-3884998	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
29	nsv878472	chr4:3414654-3451109	Weak transcription Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
30	nsv878473	chr4:3414654-3473139	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
31	esv1816543	chr4:3414654-3942867	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3391800-3424200	Weak transcription	Colonic Mucosa	Colon
2	chr4:3399200-3432200	Weak transcription	Right Atrium	heart
3	chr4:3405200-3418800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr4:3408800-3436600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr4:3411000-3436400	Strong transcription	Fetal Intestine Small	intestine
6	chr4:3411200-3436400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr4:3411200-3436600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:3411400-3425600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr4:3411800-3420000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:3413200-3420000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:3413600-3418600	Weak transcription	Thymus	Thymus
12	chr4:3413600-3437000	Strong transcription	Esophagus	oesophagus
13	chr4:3414400-3418800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:3414400-3419600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:3415000-3435600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:3415000-3436400	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr4:3415400-3437000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:3415600-3426000	Strong transcription	HepG2	liver
19	chr4:3415600-3433600	Weak transcription	Fetal Kidney	kidney
20	chr4:3415800-3418600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:3415800-3418800	Genic enhancers	Fetal Muscle Leg	muscle
22	chr4:3415800-3419600	Weak transcription	Fetal Heart	heart
23	chr4:3415800-3421800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr4:3415800-3436400	Strong transcription	Lung	lung
25	chr4:3416000-3420600	Strong transcription	Right Ventricle	heart
26	chr4:3416200-3418600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr4:3416200-3419400	Strong transcription	Liver	Liver
28	chr4:3416200-3419600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr4:3416200-3419600	Strong transcription	Brain Germinal Matrix	brain
30	chr4:3416200-3423000	Strong transcription	Fetal Stomach	stomach
31	chr4:3416400-3436200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr4:3416400-3436800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:3416600-3419400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:3416600-3423400	Weak transcription	Primary B cells from cord blood	blood
35	chr4:3416600-3423600	Weak transcription	Brain Angular Gyrus	brain
36	chr4:3416600-3428200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr4:3416600-3435600	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr4:3416600-3437800	Weak transcription	Stomach Mucosa	stomach
39	chr4:3416800-3418800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr4:3416800-3419000	Genic enhancers	Fetal Muscle Trunk	muscle
41	chr4:3416800-3420600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr4:3416800-3420800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr4:3416800-3432000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr4:3416800-3436600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr4:3416800-3438400	Weak transcription	NHDF-Ad	bronchial
46	chr4:3417000-3418600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr4:3417000-3418800	Weak transcription	NH-A	brain
48	chr4:3417000-3420600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr4:3417000-3420600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr4:3417000-3422800	Weak transcription	Fetal Thymus	thymus

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