Variant report

Variant	rs7742678
Chromosome Location	chr6:163848559-163848560
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	RAD21	chr6:163848487-163849577	SK-N-SH	brain:	n/a	n/a
2	SMC3	chr6:163848507-163849547	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr6:163848540-163849473	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:163846486..163849719-chr6:163934600..163936577,3	K562	blood:
2	chr6:163846244..163848845-chr6:163849876..163852594,2	MCF-7	breast:
3	chr6:163833988..163836212-chr6:163848529..163850044,2	MCF-7	breast:
4	chr6:163842546..163846148-chr6:163847006..163850145,4	K562	blood:

Variant related genes	Relation type
QKI	TF binding region
ENSG00000270419	Chromatin interaction
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12110648	1.00[AMR][1000 genomes]
rs56377162	1.00[AMR][1000 genomes]
rs6934643	1.00[AMR][1000 genomes]
rs6939555	1.00[AMR][1000 genomes]
rs6939751	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73784468	1.00[AMR][1000 genomes]
rs73784479	1.00[AMR][1000 genomes]
rs73787632	1.00[AMR][1000 genomes]
rs7753923	1.00[AMR][1000 genomes]
rs7765302	1.00[AMR][1000 genomes]
rs9784871	1.00[AMR][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	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1797109	chr6:163834147-163908115	Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1019551	chr6:163842358-163965216	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163837400-163857200	Weak transcription	Spleen	Spleen
2	chr6:163837800-163851000	Weak transcription	Small Intestine	intestine
3	chr6:163838000-163851600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:163838000-163860600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr6:163839800-163851600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:163840800-163865000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr6:163840800-163881400	Weak transcription	Fetal Stomach	stomach
8	chr6:163841600-163848600	Weak transcription	HMEC	breast
9	chr6:163841600-163853200	Enhancers	Adipose Nuclei	Adipose
10	chr6:163841600-163858600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:163841600-163864400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:163841800-163848600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr6:163841800-163851000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:163842000-163850000	Weak transcription	HSMMtube	muscle
15	chr6:163842200-163851000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr6:163842400-163849800	Weak transcription	Primary T cells from cord blood	blood
17	chr6:163842600-163865200	Weak transcription	Fetal Kidney	kidney
18	chr6:163843200-163848600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr6:163843800-163856200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr6:163843800-163862600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:163844200-163853600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:163844200-163860400	Weak transcription	Lung	lung
23	chr6:163844600-163848600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:163844600-163848800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:163844600-163850800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:163844600-163851000	Weak transcription	Gastric	stomach
27	chr6:163844800-163849200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:163845000-163848600	Weak transcription	A549	lung
29	chr6:163845400-163848600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr6:163845400-163848600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:163845400-163851600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:163845400-163877800	Weak transcription	Fetal Muscle Leg	muscle
33	chr6:163845600-163848600	Weak transcription	NHLF	lung
34	chr6:163846000-163850000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr6:163846000-163861600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:163846400-163849800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:163846400-163850800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:163846400-163851000	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr6:163846400-163860000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:163847000-163849600	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr6:163847000-163853200	Enhancers	Liver	Liver
42	chr6:163847200-163850600	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr6:163847400-163848800	Enhancers	Ovary	ovary
44	chr6:163847400-163848800	Enhancers	Right Ventricle	heart
45	chr6:163847400-163852000	Enhancers	Rectal Smooth Muscle	rectum
46	chr6:163847400-163852600	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr6:163847400-163853200	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr6:163847600-163848800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr6:163847600-163853200	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr6:163847800-163848600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links