Variant report

Variant	rs3757234
Chromosome Location	chr6:109706290-109706291
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:109702256-109706422	HepG2	liver:	n/a	n/a
2	KAP1	chr6:109705512-109706322	U2OS	brain:	n/a	n/a
3	GATA1	chr6:109705267-109707231	K562	blood:	n/a	chr6:109706045-109706055 chr6:109706324-109706332
4	JUN	chr6:109705357-109706403	K562	blood:	n/a	n/a
5	KAP1	chr6:109705431-109706503	HEK293	kidney:	n/a	n/a
6	TCF7L2	chr6:109705556-109706343	HepG2	liver:	n/a	n/a
7	JUND	chr6:109705271-109706326	K562	blood:	n/a	chr6:109705836-109705847

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:109704505..109707009-chr6:109717499..109719402,2	K562	blood:
2	chr6:109704063..109706352-chr6:109779634..109782625,2	K562	blood:
3	chr6:109554938..109560362-chr6:109702019..109707132,8	K562	blood:
4	chr6:109702383..109706611-chr6:109760202..109762116,4	K562	blood:
5	chr6:109616026..109618263-chr6:109705569..109707885,2	MCF-7	breast:
6	chr6:108878269..108881845-chr6:109702991..109706559,3	K562	blood:
7	chr6:109414834..109419474-chr6:109701430..109708028,12	K562	blood:
8	chr6:109705517..109707022-chr6:109759726..109761744,2	K562	blood:
9	chr6:109702022..109707287-chr6:109760251..109763953,8	MCF-7	breast:
10	chr6:109486803..109488708-chr6:109704418..109707103,2	K562	blood:
11	chr6:109624351..109631970-chr6:109702157..109706422,11	K562	blood:
12	chr6:109414590..109417855-chr6:109700035..109707147,9	K562	blood:
13	chr6:109623091..109628183-chr6:109700606..109706462,9	K562	blood:
14	chr6:108879178..108880841-chr6:109704177..109706752,2	MCF-7	breast:

No data

Variant related genes	Relation type
CD164	TF binding region
ENSG00000243587	Chromatin interaction
ENSG00000201023	Chromatin interaction
ENSG00000203799	Chromatin interaction
ENSG00000118689	Chromatin interaction
ENSG00000080546	Chromatin interaction
ENSG00000183137	Chromatin interaction
ENSG00000185250	Chromatin interaction
ENSG00000135587	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10080429	0.93[EUR][1000 genomes]
rs1040284	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10457190	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10457194	0.86[CHB][hapmap]
rs10457195	0.86[CHB][hapmap]
rs1048203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10782161	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10782162	0.95[CEU][hapmap];0.81[CHB][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10872032	0.94[EUR][1000 genomes]
rs10872034	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11153171	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs11153174	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11153175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11153176	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11153177	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11153180	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11153181	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11153183	0.86[CHB][hapmap]
rs11753645	0.81[CEU][hapmap]
rs11754455	0.86[CHB][hapmap]
rs11967108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12190920	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12190996	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12192847	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12193493	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12194061	0.86[CHB][hapmap]
rs12197114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12197180	0.86[CHB][hapmap]
rs12198938	0.86[CHB][hapmap]
rs12199154	0.86[CHB][hapmap]
rs12206928	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12208933	0.95[CEU][hapmap];0.81[CHB][hapmap]
rs12209691	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12212476	0.86[CHB][hapmap]
rs12213313	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12524273	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12524639	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528712	0.85[CEU][hapmap]
rs12528822	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13195517	0.85[CEU][hapmap]
rs13203252	0.84[CEU][hapmap]
rs13212766	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13220915	0.86[CHB][hapmap]
rs1322816	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1358997	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1358998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1406899	0.86[CHB][hapmap]
rs1546980	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1590306	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17070580	0.95[CEU][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs1923725	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2024850	0.86[CHB][hapmap]
rs2236582	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2275650	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2277114	0.86[CHB][hapmap]
rs34202013	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35056702	0.93[EUR][1000 genomes]
rs36035949	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36099706	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778475	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778477	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3799835	0.82[CEU][hapmap]
rs3799839	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3807005	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3818934	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59056467	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59906308	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68042406	0.85[EUR][1000 genomes]
rs6911838	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs6920962	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs6929023	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7372	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs752262	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7754650	0.86[YRI][hapmap]
rs7755941	0.90[CHB][hapmap]
rs7773095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773950	0.86[CHB][hapmap]
rs9320287	0.95[CEU][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs9480933	0.93[EUR][1000 genomes]
rs9480948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480951	0.93[EUR][1000 genomes]
rs9480953	0.95[CEU][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs9480955	0.93[EUR][1000 genomes]
rs9480957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9487068	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9487094	0.95[CEU][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs9487095	0.93[EUR][1000 genomes]
rs9487097	0.89[EUR][1000 genomes]
rs9487098	0.90[EUR][1000 genomes]
rs9487100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9885646	0.95[CEU][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3757234	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs3757234	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs3757234	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs3757234	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs3757234	SMPD2	cis	Whole Blood	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109703800-109707000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:109704400-109706400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr6:109704600-109706400	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr6:109704600-109706400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:109704600-109706400	Flanking Active TSS	Hela-S3	cervix
6	chr6:109704600-109706400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr6:109704600-109706600	Enhancers	Brain Cingulate Gyrus	brain
8	chr6:109704600-109706600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:109704600-109706800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:109704600-109710800	Weak transcription	Aorta	Aorta
11	chr6:109704800-109706600	Flanking Active TSS	K562	blood
12	chr6:109705000-109706400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:109705000-109706400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:109705000-109706400	Enhancers	Primary B cells from cord blood	blood
15	chr6:109705000-109706400	Enhancers	Brain Substantia Nigra	brain
16	chr6:109705000-109706400	Enhancers	Osteobl	bone
17	chr6:109705000-109706600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:109705000-109706600	Enhancers	Fetal Thymus	thymus
19	chr6:109705000-109707000	Enhancers	Stomach Mucosa	stomach
20	chr6:109705000-109707600	Enhancers	Placenta	Placenta
21	chr6:109705000-109745200	Weak transcription	Fetal Kidney	kidney
22	chr6:109705200-109706400	Enhancers	Primary B cells from peripheral blood	blood
23	chr6:109705200-109706400	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr6:109705200-109706400	Enhancers	A549	lung
25	chr6:109705200-109706600	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr6:109705200-109706600	Enhancers	Fetal Stomach	stomach
27	chr6:109705200-109710800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr6:109705400-109707000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:109705400-109707800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:109705400-109710800	Weak transcription	Right Atrium	heart
31	chr6:109705600-109706400	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr6:109705600-109706600	Enhancers	Adipose Nuclei	Adipose
33	chr6:109705600-109706600	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr6:109705600-109707000	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr6:109705800-109706400	Enhancers	Small Intestine	intestine
36	chr6:109705800-109706600	Flanking Active TSS	HepG2	liver
37	chr6:109705800-109706800	Enhancers	Gastric	stomach
38	chr6:109705800-109707400	Weak transcription	HSMMtube	muscle
39	chr6:109705800-109711000	Weak transcription	Primary T cells from cord blood	blood
40	chr6:109705800-109711000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr6:109706000-109706400	Enhancers	Muscle Satellite Cultured Cells	--
42	chr6:109706000-109706400	Enhancers	Liver	Liver
43	chr6:109706000-109706400	Enhancers	Colon Smooth Muscle	Colon
44	chr6:109706000-109706400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr6:109706000-109706400	Enhancers	NHEK	skin
46	chr6:109706000-109706800	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr6:109706000-109706800	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr6:109706000-109710800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:109706000-109710800	Weak transcription	Left Ventricle	heart
50	chr6:109706000-109711600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links