Variant report

Variant	rs6674688
Chromosome Location	chr1:171699030-171699031
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171621375..171623706-chr1:171697958..171699845,2	K562	blood:
2	chr1:171696496..171698360-chr1:171698518..171700824,2	K562	blood:

Variant related genes	Relation type
ENSG00000034971	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10798598	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10798599	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10798603	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10913488	0.80[EUR][1000 genomes]
rs10913508	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10913530	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913559	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10913578	0.83[GIH][hapmap];0.86[YRI][hapmap]
rs10913586	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11583530	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11805692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11806314	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12045452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12096984	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12120152	0.82[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12139610	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16843251	0.90[YRI][hapmap]
rs2073484	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2227229	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3753539	0.83[GIH][hapmap];0.86[YRI][hapmap]
rs4342884	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4468194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425400	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6659539	0.81[EUR][1000 genomes]
rs6662836	0.95[CEU][hapmap];0.84[JPT][hapmap]
rs6665581	1.00[CEU][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6668623	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6672082	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6673782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6674468	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6674774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682452	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6685742	0.90[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6688447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6700606	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs763225	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9659578	1.00[CEU][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap]
rs9943293	1.00[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap]
rs999685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv12447	chr1:171556291-171726822	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv1800458	chr1:171667663-171701129	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6674688	DNM3	cis	cerebellum	SCAN
rs6674688	METTL13	cis	parietal	SCAN
rs6674688	PRDX6	cis	parietal	SCAN
rs6674688	VAMP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171665600-171705600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:171665600-171708800	Weak transcription	Brain Angular Gyrus	brain
3	chr1:171666000-171705400	Weak transcription	Pancreas	Pancrea
4	chr1:171666800-171702400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:171668800-171705400	Weak transcription	Right Ventricle	heart
6	chr1:171668800-171708200	Weak transcription	Small Intestine	intestine
7	chr1:171669600-171705400	Weak transcription	Fetal Brain Male	brain
8	chr1:171686600-171710400	Weak transcription	Esophagus	oesophagus
9	chr1:171686600-171710400	Weak transcription	Gastric	stomach
10	chr1:171686800-171704600	Weak transcription	NHEK	skin
11	chr1:171687000-171704600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:171687600-171704600	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:171687600-171708000	Weak transcription	K562	blood
14	chr1:171692400-171705800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:171692400-171708400	Weak transcription	Brain Substantia Nigra	brain
16	chr1:171692400-171710400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:171692400-171710400	Weak transcription	Lung	lung
18	chr1:171692600-171705000	Weak transcription	Thymus	Thymus
19	chr1:171692600-171705400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:171692600-171705600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:171692600-171708400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:171692600-171709800	Weak transcription	Stomach Mucosa	stomach
23	chr1:171692600-171710200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:171692800-171704800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:171692800-171705600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:171693200-171705000	Weak transcription	Fetal Intestine Small	intestine
27	chr1:171693200-171705400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:171693200-171709800	Weak transcription	Fetal Kidney	kidney
29	chr1:171694200-171699200	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr1:171694200-171699400	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:171694400-171700000	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr1:171694400-171705200	Weak transcription	A549	lung
33	chr1:171694800-171704600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:171694800-171704800	Weak transcription	GM12878-XiMat	blood
35	chr1:171694800-171709000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:171695000-171710400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:171695400-171699600	Strong transcription	Primary T cells from cord blood	blood
38	chr1:171695600-171699400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:171695600-171699400	Strong transcription	Fetal Thymus	thymus
40	chr1:171695600-171708400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr1:171695800-171699200	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr1:171695800-171699600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:171696000-171699200	Strong transcription	Fetal Intestine Large	intestine
44	chr1:171696000-171699600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:171696000-171700400	Weak transcription	Fetal Heart	heart
46	chr1:171696000-171710200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr1:171696200-171710400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr1:171696400-171699800	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr1:171696400-171704600	Weak transcription	Fetal Muscle Leg	muscle
50	chr1:171696400-171709800	Weak transcription	Psoas Muscle	Psoas

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