Variant report

Variant	rs13101346
Chromosome Location	chr4:144283155-144283156
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:144280022..144283375-chr4:144285064..144288406,3	K562	blood:
2	chr4:144274310..144276106-chr4:144283049..144285599,2	MCF-7	breast:
3	chr4:144272912..144279199-chr4:144279482..144284125,11	K562	blood:
4	chr4:144275276..144278433-chr4:144281060..144283410,4	MCF-7	breast:
5	chr4:144282645..144284355-chr4:144296664..144298307,2	MCF-7	breast:
6	chr4:144256496..144258835-chr4:144281268..144283636,2	MCF-7	breast:
7	chr4:144257782..144259357-chr4:144281420..144283250,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178972	Chromatin interaction
ENSG00000109458	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10013047	0.96[ASN][1000 genomes]
rs1027851	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1027852	0.96[ASN][1000 genomes]
rs11100786	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11100787	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11100788	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11100789	0.81[ASN][1000 genomes]
rs11730569	0.95[ASN][1000 genomes]
rs11945731	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12647531	0.95[ASN][1000 genomes]
rs12649592	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13123498	0.94[ASN][1000 genomes]
rs1397526	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1397527	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1397528	0.82[ASN][1000 genomes]
rs1472873	0.95[ASN][1000 genomes]
rs1510879	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1510880	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1866756	0.96[ASN][1000 genomes]
rs2048408	0.94[ASN][1000 genomes]
rs2055730	0.95[ASN][1000 genomes]
rs2119270	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2196908	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2196909	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs300910	0.90[ASN][1000 genomes]
rs300911	0.87[ASN][1000 genomes]
rs300912	0.87[ASN][1000 genomes]
rs300913	0.87[ASN][1000 genomes]
rs300914	0.87[ASN][1000 genomes]
rs300915	0.87[ASN][1000 genomes]
rs300916	0.84[ASN][1000 genomes]
rs300917	0.83[ASN][1000 genomes]
rs300918	0.83[ASN][1000 genomes]
rs34095331	0.85[ASN][1000 genomes]
rs34439737	0.89[ASN][1000 genomes]
rs3792652	0.96[ASN][1000 genomes]
rs3792653	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3792655	0.95[ASN][1000 genomes]
rs3805238	0.84[ASN][1000 genomes]
rs3805245	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3805246	0.95[ASN][1000 genomes]
rs3805247	0.96[ASN][1000 genomes]
rs3805249	0.95[ASN][1000 genomes]
rs3805251	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805252	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805253	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805254	0.95[ASN][1000 genomes]
rs3805256	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805257	0.97[ASN][1000 genomes]
rs3828512	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3828513	0.95[ASN][1000 genomes]
rs3828514	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55758499	0.95[ASN][1000 genomes]
rs55894236	0.95[ASN][1000 genomes]
rs6537154	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6537155	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs713140	0.93[ASN][1000 genomes]
rs719392	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7679870	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7680959	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs906571	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033902	chr4:144114413-144285772	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1026110	chr4:144239825-144292148	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:144272800-144284600	Enhancers	Fetal Intestine Small	intestine
2	chr4:144272800-144299800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr4:144276400-144286000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:144276800-144284800	Weak transcription	Lung	lung
5	chr4:144277200-144284000	Enhancers	Fetal Intestine Large	intestine
6	chr4:144277200-144290400	Weak transcription	Pancreas	Pancrea
7	chr4:144277400-144296800	Weak transcription	HSMMtube	muscle
8	chr4:144278200-144285400	Enhancers	Fetal Heart	heart
9	chr4:144279000-144283600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:144279600-144284200	Enhancers	Brain Anterior Caudate	brain
11	chr4:144279800-144283400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr4:144279800-144286000	Enhancers	Brain Cingulate Gyrus	brain
13	chr4:144280000-144283200	Enhancers	Placenta Amnion	Placenta Amnion
14	chr4:144280000-144283400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr4:144280200-144285400	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr4:144280400-144284400	Enhancers	Colon Smooth Muscle	Colon
17	chr4:144280400-144285600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:144280800-144283800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr4:144280800-144286000	Enhancers	Brain Hippocampus Middle	brain
20	chr4:144281000-144283800	Weak transcription	Right Atrium	heart
21	chr4:144281200-144283400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr4:144281200-144283800	Weak transcription	Spleen	Spleen
23	chr4:144281200-144284400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:144281200-144284600	Weak transcription	Placenta	Placenta
25	chr4:144281200-144285200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:144281200-144285400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr4:144281200-144285400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr4:144281200-144290000	Weak transcription	Fetal Stomach	stomach
29	chr4:144281200-144296800	Weak transcription	Fetal Muscle Leg	muscle
30	chr4:144281400-144296800	Weak transcription	Fetal Kidney	kidney
31	chr4:144281600-144283400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr4:144281600-144283400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:144281800-144284200	Enhancers	Duodenum Mucosa	Duodenum
34	chr4:144281800-144286000	Enhancers	Brain Substantia Nigra	brain
35	chr4:144281800-144293400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:144282000-144284800	Enhancers	Brain Angular Gyrus	brain
37	chr4:144282000-144291200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:144282200-144283600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr4:144282200-144284200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:144282200-144284200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:144282200-144285600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr4:144282400-144283400	Weak transcription	HUVEC	blood vessel
43	chr4:144282400-144284600	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr4:144282400-144285400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr4:144282600-144283400	Enhancers	Psoas Muscle	Psoas
46	chr4:144282600-144283800	Weak transcription	NH-A	brain
47	chr4:144282600-144284000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr4:144282600-144284000	Enhancers	Fetal Thymus	thymus
49	chr4:144282600-144284600	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr4:144282600-144285000	Enhancers	Small Intestine	intestine

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