Variant report

Variant	rs240402
Chromosome Location	chr6:75983357-75983358
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr6:75983302-75983365	GM12878	blood:	n/a	n/a
2	GATA3	chr6:75982963-75983500	SH-SY5Y	brain:	n/a	n/a
3	MAFK	chr6:75983149-75983405	HepG2	liver:	n/a	chr6:75983249-75983263 chr6:75983246-75983262 chr6:75983251-75983262 chr6:75983251-75983262 chr6:75983250-75983261

No.	Distal block	Cell Line	Cell type
1	chr6:75953197..75955267-chr6:75981448..75984407,2	K562	blood:
2	chr6:75981554..75983680-chr6:75993870..75995991,2	K562	blood:
3	chr6:75982180..75984876-chr6:75993848..75995841,3	K562	blood:

Variant related genes	Relation type
TMEM30A	TF binding region
ENSG00000225793	Chromatin interaction
ENSG00000112695	Chromatin interaction
ENSG00000112697	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs117512	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203213	0.89[EUR][1000 genomes]
rs147523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15616	0.87[EUR][1000 genomes]
rs240361	1.00[JPT][hapmap]
rs240367	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs240368	0.91[EUR][1000 genomes]
rs240369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs240381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240382	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs240383	0.85[EUR][1000 genomes]
rs240385	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240388	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs240389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240390	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs240392	0.87[EUR][1000 genomes]
rs240393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240400	0.87[EUR][1000 genomes]
rs240401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240404	1.00[EUR][1000 genomes]
rs240405	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs240409	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs240410	0.84[EUR][1000 genomes]
rs240423	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs240428	0.87[EUR][1000 genomes]
rs240429	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240430	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240431	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs240432	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs2842455	0.83[YRI][hapmap]
rs381141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs397039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414624	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs418485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs429746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs448854	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs542717	0.91[EUR][1000 genomes]
rs638590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643707	0.94[EUR][1000 genomes]
rs654428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs683943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928694	0.85[YRI][hapmap]
rs73453705	0.92[AFR][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	nsv1016804	chr6:75775846-76188585	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538310	chr6:75775846-76188585	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1024079	chr6:75848556-76238519	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	nsv603763	chr6:75923605-76009426	Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv603764	chr6:75963751-76025603	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv830698	chr6:75968810-76115592	Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75954400-75986000	Weak transcription	Brain Germinal Matrix	brain
2	chr6:75954800-75988200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:75967800-75988200	Weak transcription	Fetal Brain Male	brain
4	chr6:75969600-75983800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr6:75969600-75992200	Weak transcription	Colonic Mucosa	Colon
6	chr6:75970000-75992400	Weak transcription	Brain Substantia Nigra	brain
7	chr6:75973000-75985200	Weak transcription	HepG2	liver
8	chr6:75973200-75985000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:75973400-75985600	Weak transcription	Lung	lung
10	chr6:75973400-75988200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:75974000-75986200	Weak transcription	K562	blood
12	chr6:75974000-75988000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:75974200-75993000	Weak transcription	Placenta	Placenta
14	chr6:75974800-75989800	Weak transcription	Fetal Brain Female	brain
15	chr6:75975000-75988200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr6:75975000-75992400	Weak transcription	Fetal Stomach	stomach
17	chr6:75978200-75989400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr6:75978200-75992400	Weak transcription	Fetal Kidney	kidney
19	chr6:75978400-75990000	Weak transcription	Fetal Intestine Small	intestine
20	chr6:75978600-75984800	Weak transcription	Hela-S3	cervix
21	chr6:75978600-75985600	Weak transcription	Left Ventricle	heart
22	chr6:75978600-75985600	Weak transcription	Right Ventricle	heart
23	chr6:75978600-75993600	Weak transcription	Esophagus	oesophagus
24	chr6:75979000-75984200	Weak transcription	Psoas Muscle	Psoas
25	chr6:75979000-75986400	Weak transcription	Gastric	stomach
26	chr6:75979800-75983400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:75979800-75984400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:75979800-75984400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
29	chr6:75979800-75986200	ZNF genes & repeats	GM12878-XiMat	blood
30	chr6:75980000-75984400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:75980200-75983400	Strong transcription	HSMM	muscle
32	chr6:75981000-75984000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
33	chr6:75981400-75983400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:75981400-75984000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr6:75981800-75983600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr6:75981800-75984000	Genic enhancers	Dnd41	blood
37	chr6:75982000-75983400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
38	chr6:75982200-75983400	ZNF genes & repeats	Primary T cells from cord blood	blood
39	chr6:75982200-75983400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr6:75982200-75984400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
41	chr6:75982400-75983400	Enhancers	Small Intestine	intestine
42	chr6:75982400-75984200	Enhancers	Colon Smooth Muscle	Colon
43	chr6:75982400-75986400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:75982600-75983600	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr6:75982600-75984000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr6:75982600-75984000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:75982600-75984800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:75982600-75988000	Weak transcription	Brain Angular Gyrus	brain
49	chr6:75982600-75988200	Weak transcription	Adipose Nuclei	Adipose
50	chr6:75982600-75991800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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