Variant report

Variant	rs598855
Chromosome Location	chr1:176141866-176141867
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:176139119..176142139-chr6:26032575..26034849,4	MCF-7	breast:
2	chr1:176139139..176142119-chr6:26031592..26033955,2	K562	blood:
3	chr1:176141778..176145305-chr1:176175202..176178321,3	K562	blood:

Variant related genes	Relation type
ENSG00000137259	Chromatin interaction
ENSG00000236021	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000143207	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10429846	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798430	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798435	1.00[CHB][hapmap]
rs10913125	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481626	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481629	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481632	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481636	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2481637	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481640	1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481648	1.00[CHB][hapmap]
rs2481649	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481652	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502821	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502827	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502828	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502833	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2502837	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2774925	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233165	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4298689	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4344283	1.00[ASN][1000 genomes]
rs4347169	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4379645	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4460596	1.00[CHB][hapmap]
rs4534339	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652146	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533299	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537407	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613965	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61821055	1.00[ASN][1000 genomes]
rs6425369	1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6425372	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425373	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425374	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs646754	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs704828	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs704833	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7525112	1.00[CHB][hapmap]
rs7532122	1.00[CHB][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541563	1.00[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554913	1.00[CHB][hapmap]
rs791748	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425444	1.00[EUR][1000 genomes]
rs998631	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[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	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS 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	33 gene(s)	inside rSNPs	diseases
2	nsv872562	chr1:175949646-176141866	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv872565	chr1:176058782-176172795	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv8558	chr1:176135063-176141916	Enhancers Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:176065600-176154800	Weak transcription	Aorta	Aorta
2	chr1:176070400-176151400	Weak transcription	Pancreas	Pancrea
3	chr1:176085400-176142400	Weak transcription	Lung	lung
4	chr1:176100800-176153200	Weak transcription	Colonic Mucosa	Colon
5	chr1:176110600-176164000	Weak transcription	NHLF	lung
6	chr1:176116000-176146200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:176123800-176144200	Weak transcription	Left Ventricle	heart
8	chr1:176123800-176150000	Weak transcription	Osteobl	bone
9	chr1:176126400-176168800	Weak transcription	Small Intestine	intestine
10	chr1:176127000-176147000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:176127000-176174000	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:176127200-176153400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:176127400-176143200	Weak transcription	Brain Substantia Nigra	brain
14	chr1:176127400-176144200	Weak transcription	A549	lung
15	chr1:176127400-176153400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr1:176127400-176155400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:176128000-176144200	Weak transcription	Gastric	stomach
18	chr1:176128000-176147000	Weak transcription	Stomach Mucosa	stomach
19	chr1:176128000-176157800	Weak transcription	Spleen	Spleen
20	chr1:176128000-176175200	Weak transcription	Esophagus	oesophagus
21	chr1:176128400-176154600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:176128600-176147000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr1:176128600-176147200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr1:176128600-176155600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:176128800-176152800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:176128800-176152800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:176128800-176154200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:176130400-176143200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:176131000-176143400	Weak transcription	NHDF-Ad	bronchial
30	chr1:176131000-176144000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:176131400-176142600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:176131800-176143600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:176132200-176154200	Weak transcription	NH-A	brain
34	chr1:176132400-176143400	Weak transcription	NHEK	skin
35	chr1:176134400-176152800	Weak transcription	Brain Angular Gyrus	brain
36	chr1:176135000-176142400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr1:176135200-176144600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:176136200-176147400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:176137400-176173000	Weak transcription	Right Ventricle	heart
40	chr1:176137800-176142200	Strong transcription	Primary B cells from peripheral blood	blood
41	chr1:176137800-176142200	Strong transcription	HSMM	muscle
42	chr1:176138200-176155800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr1:176138600-176142600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:176138600-176143000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:176138600-176146200	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr1:176138800-176142200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
47	chr1:176138800-176142800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:176138800-176143000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:176138800-176143000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr1:176138800-176143000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links