Variant report

Variant	rs4146297
Chromosome Location	chr6:144839344-144839345
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1005974	0.91[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1016235	0.83[EUR][1000 genomes]
rs10434891	0.82[JPT][hapmap]
rs11155357	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11155361	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs12196553	0.82[JPT][hapmap]
rs12201476	0.83[EUR][1000 genomes]
rs12204372	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12214126	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13191597	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs13193448	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs13195928	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13198102	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13201946	0.82[EUR][1000 genomes]
rs13203229	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs13203387	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13205040	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13207331	0.84[ASN][1000 genomes]
rs13211138	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1534437	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1554813	0.83[EUR][1000 genomes]
rs1554814	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1554816	0.89[MEX][hapmap];0.81[TSI][hapmap]
rs1590055	0.82[EUR][1000 genomes]
rs17793810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1830271	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs1918744	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs1918745	0.83[EUR][1000 genomes]
rs1918746	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1918747	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1918748	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2178128	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes]
rs34053805	0.81[EUR][1000 genomes]
rs34095417	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34504312	0.81[EUR][1000 genomes]
rs34571592	0.83[EUR][1000 genomes]
rs35161160	0.81[EUR][1000 genomes]
rs35524567	0.82[EUR][1000 genomes]
rs35866755	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35904953	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3811099	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3924656	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs3924657	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs4052725	0.85[EUR][1000 genomes]
rs4075776	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4401687	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs4438980	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4582403	0.86[EUR][1000 genomes]
rs56039703	0.81[EUR][1000 genomes]
rs56158631	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66905872	0.99[ASN][1000 genomes]
rs67767204	0.81[EUR][1000 genomes]
rs6908795	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6915390	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6918394	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6919793	0.83[EUR][1000 genomes]
rs6920388	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6924812	0.83[EUR][1000 genomes]
rs6938409	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6938455	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6938776	0.86[EUR][1000 genomes]
rs73001731	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73005504	0.81[EUR][1000 genomes]
rs73005509	0.81[EUR][1000 genomes]
rs73005511	0.81[EUR][1000 genomes]
rs7739143	0.82[JPT][hapmap]
rs7740593	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7753246	0.82[JPT][hapmap]
rs9376829	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs9390177	1.00[CEU][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs9390179	0.82[EUR][1000 genomes]
rs9390180	1.00[ASW][hapmap];0.81[CEU][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap]
rs9390185	0.82[ASW][hapmap]
rs9403565	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes]
rs9403566	0.82[EUR][1000 genomes]
rs9403569	1.00[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs9403570	0.82[JPT][hapmap]
rs9497023	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs952050	1.00[CEU][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs952051	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1015228	chr6:144780458-144989321	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv538462	chr6:144780458-144989321	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144795800-144849800	Weak transcription	HMEC	breast
2	chr6:144803400-144869800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:144807400-144904000	Weak transcription	Brain Substantia Nigra	brain
4	chr6:144812400-144840400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:144812400-144844800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:144812400-144881000	Weak transcription	Stomach Mucosa	stomach
7	chr6:144812600-144849600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr6:144812600-144849600	Weak transcription	NH-A	brain
9	chr6:144812600-144869800	Weak transcription	Colon Smooth Muscle	Colon
10	chr6:144813400-144850000	Weak transcription	Colonic Mucosa	Colon
11	chr6:144815000-144855400	Weak transcription	Psoas Muscle	Psoas
12	chr6:144815200-144881000	Weak transcription	NHEK	skin
13	chr6:144816600-144881400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:144821000-144844200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:144821200-144850000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:144821200-144861000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:144827200-144857200	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr6:144829000-144849800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:144829200-144849600	Weak transcription	Right Ventricle	heart
20	chr6:144829200-144849800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:144829600-144849800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:144829800-144849200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:144829800-144849600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:144829800-144849600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr6:144829800-144849600	Weak transcription	Spleen	Spleen
26	chr6:144829800-144849800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:144829800-144850000	Weak transcription	Esophagus	oesophagus
28	chr6:144829800-144854200	Weak transcription	Gastric	stomach
29	chr6:144829800-144863800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr6:144831400-144849200	Weak transcription	Fetal Heart	heart
31	chr6:144831400-144879000	Strong transcription	Primary B cells from cord blood	blood
32	chr6:144831600-144853200	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr6:144831800-144857000	Strong transcription	Primary B cells from peripheral blood	blood
34	chr6:144832000-144844800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:144832200-144856800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr6:144832400-144862200	Weak transcription	Small Intestine	intestine
37	chr6:144833400-144842200	Strong transcription	Primary hematopoietic stem cells	blood
38	chr6:144833400-144845600	Strong transcription	Fetal Thymus	thymus
39	chr6:144833400-144849600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:144833600-144839800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr6:144833800-144839600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:144833800-144839600	Strong transcription	Ovary	ovary
43	chr6:144833800-144846200	Strong transcription	HepG2	liver
44	chr6:144833800-144857000	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr6:144833800-144857200	Strong transcription	Primary T cells from cord blood	blood
46	chr6:144833800-144868200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr6:144834000-144839800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:144834000-144839800	Strong transcription	Dnd41	blood
49	chr6:144834000-144839800	Strong transcription	HUVEC	blood vessel
50	chr6:144834000-144846600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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