Variant report

Variant	rs16844124
Chromosome Location	chr4:3303460-3303461
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3298898..3300688-chr4:3301683..3304655,2	K562	blood:
2	chr4:3301249..3303803-chr4:3305446..3308056,2	MCF-7	breast:
3	chr4:3302327..3305521-chr4:3308441..3313111,5	MCF-7	breast:
4	chr4:3294026..3296810-chr4:3301953..3306532,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1120898	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13110866	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13120043	0.82[CEU][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13126960	0.82[ASN][1000 genomes]
rs13129052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13130998	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13133859	0.82[CEU][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13150521	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16844147	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16844152	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16844209	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs34004517	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34052318	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34067673	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34628563	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34780636	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34849917	0.82[ASN][1000 genomes]
rs35150150	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35450001	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35720136	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35825779	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57904538	0.91[ASN][1000 genomes]
rs61211078	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61748736	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71608266	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71608267	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71608268	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71608278	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs878004	0.82[ASN][1000 genomes]
rs994425	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs994426	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.91[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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv593440	chr4:3283422-3339038	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
13	nsv461165	chr4:3283422-3342137	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
14	nsv593441	chr4:3283422-3342137	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3294600-3308800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:3296000-3306000	Weak transcription	Colon Smooth Muscle	Colon
3	chr4:3296600-3318600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:3296800-3306800	Weak transcription	Pancreas	Pancrea
5	chr4:3298800-3306400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:3299200-3310000	Enhancers	HUVEC	blood vessel
7	chr4:3299600-3304200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:3299600-3306200	Weak transcription	Fetal Intestine Small	intestine
9	chr4:3299600-3306200	Weak transcription	NHLF	lung
10	chr4:3299600-3306600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:3299600-3318600	Weak transcription	Aorta	Aorta
12	chr4:3300600-3304400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr4:3300600-3306200	Enhancers	Brain Germinal Matrix	brain
14	chr4:3300800-3303800	Enhancers	Primary T cells from cord blood	blood
15	chr4:3300800-3303800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:3300800-3304000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr4:3300800-3304600	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr4:3300800-3305400	Enhancers	Lung	lung
19	chr4:3300800-3309000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr4:3301000-3304200	Enhancers	Spleen	Spleen
21	chr4:3301000-3310400	Enhancers	Fetal Muscle Leg	muscle
22	chr4:3301200-3303800	Enhancers	Primary T cells fromperipheralblood	blood
23	chr4:3301200-3350000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr4:3301400-3303800	Enhancers	Brain Substantia Nigra	brain
25	chr4:3301400-3306200	Weak transcription	Ovary	ovary
26	chr4:3301400-3306400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:3301400-3307000	Weak transcription	Fetal Intestine Large	intestine
28	chr4:3301600-3304800	Enhancers	Stomach Mucosa	stomach
29	chr4:3301600-3305000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:3301600-3306400	Weak transcription	Fetal Kidney	kidney
31	chr4:3301600-3312400	Enhancers	Fetal Muscle Trunk	muscle
32	chr4:3301800-3303600	Weak transcription	HSMMtube	muscle
33	chr4:3301800-3305200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:3301800-3305200	Enhancers	Gastric	stomach
35	chr4:3301800-3305400	Genic enhancers	Fetal Stomach	stomach
36	chr4:3301800-3306200	Weak transcription	Adipose Nuclei	Adipose
37	chr4:3301800-3306200	Weak transcription	Right Atrium	heart
38	chr4:3302000-3303800	Weak transcription	Placenta	Placenta
39	chr4:3302000-3304800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:3302000-3305600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:3302000-3306000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr4:3302000-3306200	Weak transcription	Left Ventricle	heart
43	chr4:3302200-3304000	Enhancers	HepG2	liver
44	chr4:3302200-3304400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:3302200-3304600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:3302200-3304600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr4:3302200-3305600	Weak transcription	Brain Angular Gyrus	brain
48	chr4:3302200-3305600	Weak transcription	Fetal Heart	heart
49	chr4:3302200-3306400	Weak transcription	Psoas Muscle	Psoas
50	chr4:3302400-3303800	Enhancers	Primary T helper naive cells from peripheral blood	blood

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