Variant report

Variant	rs6685664
Chromosome Location	chr1:61805628-61805629
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	chr1:61805404..61807718-chr1:61819195..61821796,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10493305	1.00[MEX][hapmap]
rs12087318	1.00[MEX][hapmap]
rs17122076	1.00[CHB][hapmap]
rs2474394	1.00[CHB][hapmap]
rs41327150	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6678303	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6678955	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6679119	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6685656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6686618	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6690890	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6702714	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7516903	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[LWK][hapmap]
rs7538641	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1006142	chr1:61696142-62119763	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers 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	6 gene(s)	inside rSNPs	diseases
3	nsv534980	chr1:61696142-62119763	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats 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	6 gene(s)	inside rSNPs	diseases
4	nsv916868	chr1:61700430-62119762	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS 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	6 gene(s)	inside rSNPs	diseases
5	nsv1001052	chr1:61702011-62090670	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv817402	chr1:61703965-62119762	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1010797	chr1:61703966-62125970	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv530494	chr1:61723918-62084045	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv1014023	chr1:61788310-61859074	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv534981	chr1:61788310-61859074	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:61786000-61813600	Weak transcription	Duodenum Mucosa	Duodenum
2	chr1:61801000-61818600	Weak transcription	K562	blood
3	chr1:61801200-61824600	Weak transcription	Gastric	stomach
4	chr1:61802200-61805800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:61803000-61816200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:61804000-61809000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:61804000-61809000	Weak transcription	Fetal Intestine Small	intestine
8	chr1:61804000-61813200	Weak transcription	Fetal Intestine Large	intestine
9	chr1:61804000-61813200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:61804200-61807200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:61804200-61812400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:61804200-61813200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:61804400-61808200	Weak transcription	Brain Anterior Caudate	brain
14	chr1:61804400-61808400	Weak transcription	Brain Germinal Matrix	brain
15	chr1:61804400-61808600	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:61804400-61809000	Weak transcription	Ovary	ovary
17	chr1:61804400-61809200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:61804400-61809200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:61804400-61809400	Weak transcription	Brain Substantia Nigra	brain
20	chr1:61804400-61809800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:61804400-61818200	Weak transcription	Fetal Brain Male	brain
22	chr1:61804400-61818400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:61804400-61818400	Weak transcription	Hela-S3	cervix
24	chr1:61804400-61851400	Weak transcription	Small Intestine	intestine
25	chr1:61804400-61854600	Weak transcription	Placenta	Placenta
26	chr1:61804600-61805800	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr1:61804600-61807600	Weak transcription	Psoas Muscle	Psoas
28	chr1:61804600-61808200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:61804600-61808600	Weak transcription	Fetal Kidney	kidney
30	chr1:61804600-61809000	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:61804600-61809400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:61804600-61813200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:61804600-61818200	Weak transcription	Brain Angular Gyrus	brain
34	chr1:61804800-61805800	Enhancers	Liver	Liver
35	chr1:61804800-61805800	Enhancers	HMEC	breast
36	chr1:61804800-61805800	Enhancers	NHEK	skin
37	chr1:61804800-61807200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr1:61804800-61808800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:61804800-61809000	Weak transcription	Aorta	Aorta
40	chr1:61804800-61813200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:61804800-61813200	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr1:61804800-61822800	Weak transcription	Fetal Stomach	stomach
43	chr1:61805000-61805800	Weak transcription	Fetal Heart	heart
44	chr1:61805000-61805800	Genic enhancers	HepG2	liver
45	chr1:61805000-61809200	Weak transcription	Adipose Nuclei	Adipose
46	chr1:61805000-61809400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:61805000-61810000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr1:61805000-61810200	Weak transcription	Stomach Mucosa	stomach
49	chr1:61805000-61818200	Weak transcription	A549	lung
50	chr1:61805000-61818400	Weak transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links