Variant report

Variant	rs3778221
Chromosome Location	chr6:161572084-161572085
allele	C/G
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	MAZ	chr6:161571703-161572354	K562	blood:	n/a	n/a
2	CBX3	chr6:161571624-161572505	K562	blood:	n/a	n/a
3	POLR2A	chr6:161571785-161572803	K562	blood:	n/a	n/a
4	MAX	chr6:161572061-161572498	K562	blood:	n/a	n/a
5	NR2F2	chr6:161571540-161572454	K562	blood:	n/a	n/a
6	TEAD4	chr6:161571558-161572092	K562	blood:	n/a	n/a
7	TAL1	chr6:161571630-161572173	K562	blood:	n/a	chr6:161571843-161571854 chr6:161571840-161571855 chr6:161571841-161571852
8	RCOR1	chr6:161571620-161572450	K562	blood:	n/a	n/a
9	JUND	chr6:161571717-161572281	K562	blood:	n/a	n/a
10	ZNF143	chr6:161571694-161572376	K562	blood:	n/a	chr6:161572172-161572182
11	TBL1XR1	chr6:161571743-161572303	K562	blood:	n/a	n/a
12	RCOR1	chr6:161571697-161572438	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:161570952..161573247-chr6:161574439..161576942,2	K562	blood:
2	chr6:161566821..161570627-chr6:161571928..161576334,7	K562	blood:
3	chr6:161410626..161414170-chr6:161571894..161574169,3	K562	blood:
4	chr6:161410626..161413425-chr6:161571894..161573701,2	K562	blood:
5	chr6:161564867..161570084-chr6:161571350..161575451,5	K562	blood:

Variant related genes	Relation type
AGPAT4	TF binding region
ENSG00000085511	Chromatin interaction
ENSG00000272841	Chromatin interaction
ENSG00000026652	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1001421	0.83[ASN][1000 genomes]
rs11759408	0.88[ASN][1000 genomes]
rs12110827	0.88[ASN][1000 genomes]
rs1807426	0.88[ASN][1000 genomes]
rs2009830	0.88[ASN][1000 genomes]
rs3823057	0.88[ASN][1000 genomes]
rs41268545	0.88[ASN][1000 genomes]
rs55799452	0.88[ASN][1000 genomes]
rs940520	0.83[EUR][1000 genomes]
rs9458141	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886817	chr6:161371621-161846654	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1030852	chr6:161477750-161589394	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161541000-161584600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:161542000-161585600	Weak transcription	Fetal Kidney	kidney
3	chr6:161544600-161589600	Weak transcription	Fetal Brain Male	brain
4	chr6:161545000-161584800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr6:161548400-161590800	Weak transcription	Fetal Thymus	thymus
6	chr6:161549200-161577000	Strong transcription	Fetal Brain Female	brain
7	chr6:161549200-161577400	Strong transcription	Fetal Stomach	stomach
8	chr6:161549800-161589400	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr6:161550000-161584600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr6:161550200-161577400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:161553800-161586600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr6:161554000-161574000	Weak transcription	Pancreas	Pancrea
13	chr6:161554000-161591000	Weak transcription	Colonic Mucosa	Colon
14	chr6:161555000-161585000	Weak transcription	Right Atrium	heart
15	chr6:161555800-161586600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr6:161557600-161574400	Weak transcription	Gastric	stomach
17	chr6:161557600-161581400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:161557800-161584200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr6:161558200-161577800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:161558200-161582600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:161558200-161589400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr6:161558400-161581400	Weak transcription	Colon Smooth Muscle	Colon
23	chr6:161558600-161574400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr6:161559400-161587600	Weak transcription	Fetal Intestine Large	intestine
25	chr6:161560000-161583200	Weak transcription	HMEC	breast
26	chr6:161560200-161574800	Weak transcription	Right Ventricle	heart
27	chr6:161560200-161583800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:161560400-161581400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr6:161560400-161584600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr6:161560600-161584400	Weak transcription	NHLF	lung
31	chr6:161560800-161582400	Weak transcription	HSMMtube	muscle
32	chr6:161561200-161574200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:161561600-161573600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:161561600-161573800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr6:161562000-161573600	Weak transcription	Fetal Intestine Small	intestine
36	chr6:161562600-161572800	Weak transcription	Fetal Heart	heart
37	chr6:161562600-161574200	Weak transcription	Esophagus	oesophagus
38	chr6:161563400-161573800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr6:161563400-161588200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:161564000-161574000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:161564200-161572600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:161564600-161572400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:161564800-161577000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:161566000-161577600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr6:161566200-161577400	Strong transcription	Fetal Muscle Trunk	muscle
46	chr6:161566400-161574600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr6:161566600-161577400	Strong transcription	Brain Germinal Matrix	brain
48	chr6:161567000-161577600	Strong transcription	Fetal Muscle Leg	muscle
49	chr6:161567200-161572200	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr6:161567600-161572400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links