Variant report

Variant	rs6700180
Chromosome Location	chr1:197064496-197064497
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:197055379..197060712-chr1:197061077..197065456,6	K562	blood:
2	chr1:197063964..197065535-chr1:197110090..197112434,2	K562	blood:
3	chr1:197056210..197058041-chr1:197063459..197065342,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10484502	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10737685	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10754209	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10754216	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10801589	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10801594	0.93[YRI][hapmap]
rs10922163	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1127661	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs12755054	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs1332661	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1332667	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1412635	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1611982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1615413	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1750311	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap]
rs17550014	0.91[ASN][1000 genomes]
rs17550411	0.89[ASN][1000 genomes]
rs1759016	0.93[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.84[MKK][hapmap]
rs2298882	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2336596	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2878749	0.89[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs3737110	0.89[ASN][1000 genomes]
rs3737111	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3748557	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs3762271	0.91[ASN][1000 genomes]
rs41304071	0.91[ASN][1000 genomes]
rs41308365	0.91[ASN][1000 genomes]
rs41310911	0.89[ASN][1000 genomes]
rs41310925	0.91[ASN][1000 genomes]
rs41310927	0.91[ASN][1000 genomes]
rs4244139	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56084994	0.91[ASN][1000 genomes]
rs5990	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5996	0.81[ASN][1000 genomes]
rs5998	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61819074	0.86[ASN][1000 genomes]
rs61819087	0.91[ASN][1000 genomes]
rs61819088	0.91[ASN][1000 genomes]
rs61819089	0.91[ASN][1000 genomes]
rs6677930	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs6690730	0.89[ASN][1000 genomes]
rs6702252	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs698859	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs72736469	0.81[ASN][1000 genomes]
rs72736474	0.81[ASN][1000 genomes]
rs7410943	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs7514071	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7518773	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7525490	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs857018	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs955927	0.86[ASN][1000 genomes]
rs9727516	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758990	chr1:196590837-197169772	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv427897	chr1:196590837-197169772	Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv2756880	chr1:196709223-197066074	ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	esv2757767	chr1:196977799-197169772	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv873065	chr1:197027749-197076194	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv873067	chr1:197028634-197064496	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv873068	chr1:197046782-197076194	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
9	nsv873069	chr1:197055925-197109042	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197050400-197065600	Weak transcription	Stomach Mucosa	stomach
2	chr1:197051400-197069600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:197051600-197065600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:197051600-197066200	Strong transcription	Hela-S3	cervix
5	chr1:197051800-197069800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:197052200-197064600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr1:197052200-197065400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:197052200-197065400	Weak transcription	Fetal Brain Female	brain
9	chr1:197052200-197074400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:197052200-197076200	Weak transcription	NHLF	lung
11	chr1:197052200-197083600	Weak transcription	Fetal Stomach	stomach
12	chr1:197052200-197106600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:197052200-197114200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:197052400-197065400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:197052400-197068800	Weak transcription	Primary T cells from cord blood	blood
16	chr1:197052400-197069200	Strong transcription	Fetal Thymus	thymus
17	chr1:197052600-197068600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:197052800-197067000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:197053000-197064800	Strong transcription	K562	blood
20	chr1:197053000-197066800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr1:197053000-197067000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr1:197054000-197071200	Weak transcription	Brain Germinal Matrix	brain
23	chr1:197054200-197066600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:197054200-197071200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:197054200-197113600	Weak transcription	Fetal Kidney	kidney
26	chr1:197054600-197072400	Weak transcription	Thymus	Thymus
27	chr1:197054800-197065400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:197054800-197066200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:197055000-197114200	Weak transcription	Primary B cells from cord blood	blood
30	chr1:197055200-197064600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr1:197055200-197068200	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:197055400-197069400	Strong transcription	Dnd41	blood
33	chr1:197055600-197068600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:197055600-197074000	Weak transcription	Placenta	Placenta
35	chr1:197057000-197069200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:197057200-197071800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:197057200-197073200	Weak transcription	NHEK	skin
38	chr1:197057800-197069800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:197058400-197065600	Strong transcription	NHDF-Ad	bronchial
40	chr1:197058800-197070800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr1:197059600-197069200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:197060000-197073800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr1:197060400-197071200	Weak transcription	Fetal Lung	lung
44	chr1:197060400-197072400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:197061000-197067400	Weak transcription	HSMM	muscle
46	chr1:197061000-197068800	Weak transcription	Osteobl	bone
47	chr1:197061200-197073200	Weak transcription	HepG2	liver
48	chr1:197061800-197072000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr1:197062000-197069800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:197063000-197068000	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links