Variant report

Variant	rs240405
Chromosome Location	chr6:75985276-75985277
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr6:75984695-75985358	A549	lung:	n/a	n/a
2	JUND	chr6:75984648-75985446	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr6:75984664-75985484	SK-N-SH	brain:	n/a	n/a
4	SP1	chr6:75984624-75985365	A549	lung:	n/a	n/a
5	RXRA	chr6:75984643-75985469	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr6:75984652-75985514	A549	lung:	n/a	n/a
7	MAX	chr6:75984727-75985374	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr6:75984729-75985410	SK-N-SH	brain:	n/a	n/a
9	EP300	chr6:75984648-75985447	A549	lung:	n/a	n/a
10	BCL3	chr6:75984792-75985379	A549	lung:	n/a	n/a
11	EP300	chr6:75984744-75985300	SK-N-SH_RA	brain:	n/a	n/a
12	NR2F2	chr6:75984768-75985313	MCF-7	breast:	n/a	n/a
13	FOSL2	chr6:75984725-75985324	MCF-7	breast:	n/a	n/a
14	EP300	chr6:75984777-75985356	A549	lung:	n/a	n/a
15	PBX3	chr6:75984704-75985398	SK-N-SH	brain:	n/a	n/a
16	JUND	chr6:75984657-75985486	SK-N-SH	brain:	n/a	n/a
17	GATA3	chr6:75984693-75985599	SK-N-SH	brain:	n/a	n/a
18	MAFK	chr6:75984788-75985512	IMR90	lung:	n/a	n/a
19	EP300	chr6:75984850-75985383	SK-N-SH_RA	brain:	n/a	n/a
20	TCF12	chr6:75984703-75985572	SK-N-SH	brain:	n/a	n/a
21	TCF12	chr6:75984650-75985532	SK-N-SH	brain:	n/a	n/a
22	GATA3	chr6:75984697-75985553	SK-N-SH	brain:	n/a	n/a
23	FOSL2	chr6:75984653-75985545	SK-N-SH	brain:	n/a	n/a
24	JUND	chr6:75984732-75985514	SK-N-SH	brain:	n/a	n/a
25	GATA3	chr6:75984746-75985499	MCF-7	breast:	n/a	n/a
26	EP300	chr6:75984636-75985471	SK-N-SH	brain:	n/a	n/a
27	FOS	chr6:75984822-75985295	HUVEC	blood vessel:	n/a	n/a
28	TCF12	chr6:75984675-75985437	A549	lung:	n/a	n/a
29	PBX3	chr6:75984665-75985579	SK-N-SH	brain:	n/a	n/a
30	FOS	chr6:75984796-75985294	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:75985063..75990386-chr6:75992469..75996781,11	MCF-7	breast:
2	chr6:75985223..75988429-chr6:75989694..75991807,3	MCF-7	breast:
3	chr6:75952062..75953597-chr6:75984103..75985781,2	MCF-7	breast:
4	chr6:75983517..75986641-chr6:75988092..75990242,3	MCF-7	breast:

No data

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

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs117512	0.85[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1203213	0.83[EUR][1000 genomes]
rs147523	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs15616	0.82[EUR][1000 genomes]
rs240361	1.00[JPT][hapmap]
rs240367	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs240368	0.91[EUR][1000 genomes]
rs240369	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs240381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs240382	0.82[EUR][1000 genomes]
rs240385	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs240386	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs240388	0.92[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs240389	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs240390	0.92[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs240392	0.82[EUR][1000 genomes]
rs240393	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs240396	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs240398	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs240400	0.82[EUR][1000 genomes]
rs240401	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs240402	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs240403	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs240404	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs240409	0.88[EUR][1000 genomes]
rs240419	0.81[AMR][1000 genomes]
rs240428	0.82[EUR][1000 genomes]
rs240429	0.85[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs240430	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs240431	0.82[EUR][1000 genomes]
rs240432	0.84[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs381141	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs397039	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs414624	0.82[EUR][1000 genomes]
rs418485	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs429746	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs448854	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs507912	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs542717	0.91[EUR][1000 genomes]
rs56658787	0.88[AFR][1000 genomes]
rs61570087	0.81[AFR][1000 genomes]
rs638590	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs643707	0.88[EUR][1000 genomes]
rs654428	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs683943	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73451789	0.88[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:125 , 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	chr6:75969600-75992200	Weak transcription	Colonic Mucosa	Colon
5	chr6:75970000-75992400	Weak transcription	Brain Substantia Nigra	brain
6	chr6:75973400-75985600	Weak transcription	Lung	lung
7	chr6:75973400-75988200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:75974000-75986200	Weak transcription	K562	blood
9	chr6:75974000-75988000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:75974200-75993000	Weak transcription	Placenta	Placenta
11	chr6:75974800-75989800	Weak transcription	Fetal Brain Female	brain
12	chr6:75975000-75988200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:75975000-75992400	Weak transcription	Fetal Stomach	stomach
14	chr6:75978200-75989400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:75978200-75992400	Weak transcription	Fetal Kidney	kidney
16	chr6:75978400-75990000	Weak transcription	Fetal Intestine Small	intestine
17	chr6:75978600-75985600	Weak transcription	Left Ventricle	heart
18	chr6:75978600-75985600	Weak transcription	Right Ventricle	heart
19	chr6:75978600-75993600	Weak transcription	Esophagus	oesophagus
20	chr6:75979000-75986400	Weak transcription	Gastric	stomach
21	chr6:75979800-75986200	ZNF genes & repeats	GM12878-XiMat	blood
22	chr6:75982400-75986400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:75982600-75988000	Weak transcription	Brain Angular Gyrus	brain
24	chr6:75982600-75988200	Weak transcription	Adipose Nuclei	Adipose
25	chr6:75982600-75991800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr6:75982600-75992400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr6:75982600-75993600	Weak transcription	Spleen	Spleen
28	chr6:75982800-75985400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:75982800-75985600	Weak transcription	Pancreas	Pancrea
30	chr6:75982800-75985600	Weak transcription	Right Atrium	heart
31	chr6:75982800-75986400	Weak transcription	Liver	Liver
32	chr6:75982800-75987200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:75982800-75987400	Weak transcription	Brain Hippocampus Middle	brain
34	chr6:75982800-75988000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr6:75982800-75988000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr6:75982800-75989200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr6:75982800-75990200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr6:75982800-75991800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr6:75983000-75985600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr6:75983000-75985600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr6:75983000-75985600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr6:75983000-75985600	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr6:75983000-75985600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:75983000-75985600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr6:75983000-75985800	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr6:75983000-75986400	Weak transcription	Ovary	ovary
47	chr6:75983000-75987200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr6:75983000-75987200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:75983000-75987200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr6:75983000-75987200	Weak transcription	Stomach Mucosa	stomach

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