Variant report

Variant	rs2749780
Chromosome Location	chr4:3349092-3349093
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3340328..3344216-chr4:3348593..3353492,8	K562	blood:
2	chr4:3344329..3346374-chr4:3348112..3350683,2	K562	blood:
3	chr4:3346980..3350932-chr4:3475951..3478417,3	MCF-7	breast:
4	chr4:3345570..3349550-chr4:3443309..3446675,3	MCF-7	breast:
5	chr4:3343221..3349626-chr4:3462156..3471133,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159788	Chromatin interaction
ENSG00000175920	Chromatin interaction
ENSG00000109758	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10155132	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10937924	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13104157	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13150241	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2051558	0.85[ASN][1000 genomes]
rs2071666	0.86[ASN][1000 genomes]
rs2236052	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2239725	0.84[EUR][1000 genomes]
rs2748447	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2749778	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2749781	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2749782	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2749783	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2857982	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3129308	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3129310	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3129314	0.80[ASN][1000 genomes]
rs3129316	0.82[ASN][1000 genomes]
rs3129328	0.85[EUR][1000 genomes]
rs3129334	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3135145	0.85[EUR][1000 genomes]
rs3135146	0.86[EUR][1000 genomes]
rs60181496	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60208975	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6819202	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7435601	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs881816	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs881817	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs910568	0.81[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	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	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
5	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
6	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
7	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
8	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

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3301200-3350000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:3320400-3351800	Weak transcription	Aorta	Aorta
3	chr4:3334000-3370600	Weak transcription	Right Atrium	heart
4	chr4:3339200-3353200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:3342600-3350200	Weak transcription	Pancreas	Pancrea
6	chr4:3342800-3355400	Weak transcription	Esophagus	oesophagus
7	chr4:3343800-3350200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:3344000-3352400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:3344000-3354600	Weak transcription	Right Ventricle	heart
10	chr4:3344400-3349600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr4:3344400-3349800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:3344400-3350200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:3344400-3350200	Weak transcription	Ovary	ovary
14	chr4:3344400-3350200	Weak transcription	Spleen	Spleen
15	chr4:3344400-3356400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:3344400-3362400	Weak transcription	HSMMtube	muscle
17	chr4:3344400-3367600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:3344600-3349600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr4:3344800-3350200	Weak transcription	Fetal Kidney	kidney
20	chr4:3344800-3350600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:3344800-3352600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr4:3346000-3353400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:3346200-3355800	Weak transcription	Gastric	stomach
24	chr4:3346400-3350200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr4:3346400-3353400	Weak transcription	Fetal Intestine Small	intestine
26	chr4:3346400-3353400	Weak transcription	Fetal Muscle Leg	muscle
27	chr4:3346600-3350200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:3346600-3352800	Weak transcription	Brain Germinal Matrix	brain
29	chr4:3346600-3353200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:3346600-3363800	Weak transcription	Fetal Brain Female	brain
31	chr4:3346600-3364600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr4:3347400-3349800	Weak transcription	Fetal Stomach	stomach
33	chr4:3347400-3354600	Weak transcription	Lung	lung
34	chr4:3347400-3360800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:3347400-3364800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr4:3348200-3367400	Weak transcription	Fetal Heart	heart
37	chr4:3348400-3349400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr4:3348400-3350400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr4:3348400-3350600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr4:3348400-3351400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:3348400-3353200	Weak transcription	Primary T cells from cord blood	blood
42	chr4:3348400-3353400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr4:3348400-3355000	Weak transcription	HUVEC	blood vessel
44	chr4:3348400-3355200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:3348400-3358000	Weak transcription	Fetal Lung	lung
46	chr4:3348400-3360600	Weak transcription	HSMM	muscle
47	chr4:3348400-3367600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:3348600-3349800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr4:3348600-3353400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:3348600-3353400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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