Variant report

Variant	rs16844223
Chromosome Location	chr4:3378262-3378263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3377820..3379828-chr4:3379979..3381603,2	MCF-7	breast:
2	chr4:3371026..3373421-chr4:3376199..3378430,2	K562	blood:

Variant related genes	Relation type
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11930854	1.00[EUR][1000 genomes]
rs16844136	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs16844163	1.00[CEU][hapmap]
rs16844166	1.00[CEU][hapmap]
rs16844169	1.00[CEU][hapmap]
rs16844176	1.00[CEU][hapmap]
rs16844192	1.00[EUR][1000 genomes]
rs16844195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16844204	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16844219	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16844335	1.00[CEU][hapmap]
rs16844394	1.00[EUR][1000 genomes]
rs16844398	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs363109	0.90[LWK][hapmap]
rs41329644	1.00[CEU][hapmap]
rs41347150	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[LWK][hapmap]
rs6814892	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6826787	1.00[CEU][hapmap]
rs6855975	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7657430	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7663472	1.00[EUR][1000 genomes]
rs7664128	1.00[EUR][1000 genomes]
rs7673434	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7677740	1.00[EUR][1000 genomes]
rs7681258	1.00[EUR][1000 genomes]
rs7687090	1.00[EUR][1000 genomes]
rs7691619	1.00[CEU][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3372200-3382000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr4:3372200-3386400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:3372400-3382000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:3373000-3389000	Weak transcription	Psoas Muscle	Psoas
5	chr4:3373400-3380800	Weak transcription	Brain Angular Gyrus	brain
6	chr4:3373400-3382000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr4:3373400-3388400	Weak transcription	Fetal Kidney	kidney
8	chr4:3373400-3388800	Weak transcription	Colon Smooth Muscle	Colon
9	chr4:3373800-3378600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr4:3374400-3379800	Weak transcription	Fetal Lung	lung
11	chr4:3374400-3380800	Weak transcription	Fetal Brain Male	brain
12	chr4:3374600-3378400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr4:3374600-3379800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:3374600-3380000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr4:3374800-3379600	Strong transcription	Fetal Intestine Small	intestine
16	chr4:3375000-3389200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:3375200-3379600	Weak transcription	Colonic Mucosa	Colon
18	chr4:3375200-3379600	Strong transcription	Fetal Stomach	stomach
19	chr4:3375200-3381400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:3375200-3387000	Weak transcription	Right Atrium	heart
21	chr4:3375400-3378600	Strong transcription	Pancreas	Pancrea
22	chr4:3375400-3380600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr4:3375400-3381200	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr4:3375400-3386200	Weak transcription	Right Ventricle	heart
25	chr4:3375400-3386400	Weak transcription	Brain Substantia Nigra	brain
26	chr4:3375400-3386600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr4:3375400-3389600	Weak transcription	NHLF	lung
28	chr4:3375600-3378400	Strong transcription	Ovary	ovary
29	chr4:3375600-3380000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:3375600-3380200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr4:3375600-3380600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:3375600-3381600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr4:3375600-3386200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr4:3375600-3387000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr4:3375800-3378400	Strong transcription	Gastric	stomach
36	chr4:3375800-3378800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr4:3376000-3378600	Strong transcription	Fetal Brain Female	brain
38	chr4:3376000-3381400	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr4:3376000-3381800	Weak transcription	Esophagus	oesophagus
40	chr4:3376200-3380400	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr4:3376200-3380600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr4:3376400-3378600	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr4:3376600-3378600	Genic enhancers	Fetal Muscle Trunk	muscle
44	chr4:3377200-3378600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:3377400-3378400	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr4:3377400-3378400	ZNF genes & repeats	Spleen	Spleen
47	chr4:3377400-3378600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:3377400-3381200	Strong transcription	HepG2	liver
49	chr4:3377600-3378400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:3377600-3378400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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