Variant report

Variant	rs1233617
Chromosome Location	chr6:28741162-28741163
allele	G/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	JUN	chr6:28738715-28741405	K562	blood:	n/a	n/a
2	SUZ12	chr6:28740574-28741749	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:28739783..28741376-chr6:28889070..28891885,2	MCF-7	breast:
2	chr6:28739105..28742072-chr6:28746732..28748309,2	K562	blood:
3	chr6:28739775..28742884-chr6:28756307..28759477,3	K562	blood:
4	chr6:28739291..28741599-chr6:28752490..28754377,2	K562	blood:

Variant related genes	Relation type
ENSG00000221191	TF binding region
ENSG00000204713	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1002925	0.80[EUR][1000 genomes]
rs1233576	0.82[EUR][1000 genomes]
rs1233584	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1233596	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1233601	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1233602	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1233603	0.86[ASN][1000 genomes]
rs1233605	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1233607	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233615	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233616	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1235176	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1539585	0.83[EUR][1000 genomes]
rs169683	0.82[EUR][1000 genomes]
rs1742742	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs209164	0.81[EUR][1000 genomes]
rs209171	0.82[EUR][1000 genomes]
rs209173	0.83[EUR][1000 genomes]
rs209176	0.80[EUR][1000 genomes]
rs209179	0.83[EUR][1000 genomes]
rs209184	0.82[EUR][1000 genomes]
rs209186	0.81[EUR][1000 genomes]
rs2208536	0.82[EUR][1000 genomes]
rs2754764	0.82[EUR][1000 genomes]
rs2754767	0.82[EUR][1000 genomes]
rs2765218	0.81[EUR][1000 genomes]
rs2765219	0.82[EUR][1000 genomes]
rs3131342	0.82[EUR][1000 genomes]
rs3132371	0.86[EUR][1000 genomes]
rs3132386	0.80[EUR][1000 genomes]
rs377392	0.82[EUR][1000 genomes]
rs386628	0.82[EUR][1000 genomes]
rs393431	0.80[EUR][1000 genomes]
rs526983	0.83[EUR][1000 genomes]
rs7772289	0.81[EUR][1000 genomes]
rs9257134	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9257135	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28740000-28746000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:28740200-28741800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
3	chr6:28740200-28742000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr6:28740400-28741200	Bivalent Enhancer	NHEK	skin
5	chr6:28740400-28741400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:28740400-28741800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
7	chr6:28740400-28745200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:28740600-28741200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
9	chr6:28740600-28741200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:28740600-28741400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr6:28740600-28741400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:28740800-28741200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:28740800-28741200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
14	chr6:28740800-28741200	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:28740800-28741200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
16	chr6:28740800-28741200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:28740800-28741200	Bivalent Enhancer	Aorta	Aorta
18	chr6:28740800-28741400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:28740800-28741400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
20	chr6:28740800-28741400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
21	chr6:28740800-28741400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr6:28740800-28741600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
23	chr6:28740800-28741600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
24	chr6:28740800-28741600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:28740800-28741600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
26	chr6:28740800-28741600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
27	chr6:28740800-28741800	Bivalent Enhancer	Fetal Muscle Leg	muscle
28	chr6:28740800-28744400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr6:28741000-28741200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:28741000-28741200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:28741000-28741200	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr6:28741000-28741200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:28741000-28741200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:28741000-28741200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:28741000-28741200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:28741000-28741200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr6:28741000-28741200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
38	chr6:28741000-28741200	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
39	chr6:28741000-28741200	Bivalent Enhancer	Fetal Heart	heart
40	chr6:28741000-28741200	Bivalent Enhancer	Fetal Intestine Small	intestine
41	chr6:28741000-28741200	Bivalent Enhancer	Fetal Lung	lung
42	chr6:28741000-28741200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
43	chr6:28741000-28741200	Bivalent Enhancer	Right Ventricle	heart
44	chr6:28741000-28741200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
45	chr6:28741000-28741200	Enhancers	K562	blood
46	chr6:28741000-28741400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:28741000-28741400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:28741000-28741400	Bivalent Enhancer	HepG2	liver
49	chr6:28741000-28741600	Bivalent Enhancer	Fetal Stomach	stomach
50	chr6:28741000-28745000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell

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