Variant report

Variant	rs16843454
Chromosome Location	chr4:2849235-2849236
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:2843889..2847586-chr4:2849028..2855037,6	K562	blood:
2	chr4:2847502..2850014-chr4:2935362..2937925,4	MCF-7	breast:
3	chr4:2848510..2850735-chr4:2868206..2870939,2	K562	blood:
4	chr4:2843310..2847623-chr4:2847879..2851865,7	K562	blood:
5	chr4:2842030..2853279-chr4:2934021..2940851,24	MCF-7	breast:
6	chr4:2821326..2822981-chr4:2847695..2849369,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000087266	Chromatin interaction
ENSG00000087274	Chromatin interaction
ENSG00000249673	Chromatin interaction
ENSG00000109736	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1034400	1.00[ASN][1000 genomes]
rs10488838	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1263331	1.00[ASN][1000 genomes]
rs1574473	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843169	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843481	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843500	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843535	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843539	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843553	1.00[ASN][1000 genomes]
rs16843596	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2005451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857845	1.00[ASN][1000 genomes]
rs34120252	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34241425	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34550139	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34585460	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34743278	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34745961	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34945392	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35445752	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35508581	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35893718	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35913891	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36038921	1.00[ASN][1000 genomes]
rs41528047	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4741	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4969	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56975682	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57155428	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57174035	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57557041	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57763208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58059873	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58132256	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58196520	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58731679	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58758786	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58928665	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59426248	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59786983	1.00[ASN][1000 genomes]
rs59790260	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59798370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60169711	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61117606	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61339714	0.87[EUR][1000 genomes];1.00[ASN][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	nsv878444	chr4:2689449-2861090	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv878450	chr4:2760222-2861090	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv593435	chr4:2770772-2881256	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv878451	chr4:2785556-2856687	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1010533	chr4:2792848-2873441	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv521858	chr4:2846799-2881256	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2846400-2851000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:2846600-2854400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:2846600-2862400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:2846800-2849400	Enhancers	Primary hematopoietic stem cells	blood
5	chr4:2846800-2851000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:2846800-2854200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:2846800-2855400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr4:2846800-2855400	Weak transcription	Placenta	Placenta
9	chr4:2846800-2855600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr4:2846800-2857400	Weak transcription	Aorta	Aorta
11	chr4:2846800-2861800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr4:2846800-2861800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr4:2846800-2862000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:2846800-2862600	Weak transcription	Esophagus	oesophagus
15	chr4:2847000-2849600	Weak transcription	Gastric	stomach
16	chr4:2847000-2850600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:2847000-2851000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:2847200-2849400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr4:2847200-2849600	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr4:2847200-2849600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr4:2847200-2850200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:2847200-2850400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr4:2847200-2850800	Weak transcription	Fetal Brain Female	brain
24	chr4:2847200-2851200	Weak transcription	HSMM	muscle
25	chr4:2847200-2852000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr4:2847200-2853600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr4:2847200-2862200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr4:2847400-2849400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr4:2847400-2849400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:2847400-2849400	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr4:2847400-2849400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:2847400-2849400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:2847400-2849400	Weak transcription	Colonic Mucosa	Colon
34	chr4:2847400-2849400	Weak transcription	Ovary	ovary
35	chr4:2847400-2849400	Weak transcription	Thymus	Thymus
36	chr4:2847400-2849600	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr4:2847400-2850000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr4:2847400-2850200	Weak transcription	Psoas Muscle	Psoas
39	chr4:2847400-2850400	Weak transcription	Fetal Intestine Large	intestine
40	chr4:2847400-2850400	Weak transcription	NHDF-Ad	bronchial
41	chr4:2847400-2851000	Weak transcription	Right Atrium	heart
42	chr4:2847400-2851000	Weak transcription	HSMMtube	muscle
43	chr4:2847400-2852800	Weak transcription	Fetal Thymus	thymus
44	chr4:2847400-2854400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr4:2847400-2854400	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr4:2847400-2859800	Weak transcription	A549	lung
47	chr4:2847400-2863600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr4:2847600-2849400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:2847600-2849400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr4:2847800-2849400	Weak transcription	Stomach Smooth Muscle	stomach

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