Variant report

Variant	rs41274961
Chromosome Location	chr9:103111418-103111419
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	chr9:103108891..103111879-chr9:103188016..103191736,3	K562	blood:
2	chr9:103108889..103112022-chr9:103112659..103116565,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136891	Chromatin interaction
ENSG00000066697	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10819755	0.86[EUR][1000 genomes]
rs10819757	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10819758	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819760	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819765	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819766	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819768	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989041	0.92[EUR][1000 genomes]
rs10989046	0.92[EUR][1000 genomes]
rs10989047	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989050	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989051	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989062	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989063	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989068	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989072	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989077	1.00[ASN][1000 genomes]
rs11515449	0.91[EUR][1000 genomes]
rs11515542	0.91[EUR][1000 genomes]
rs11788648	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11790431	0.92[EUR][1000 genomes]
rs11791637	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11791943	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11793726	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11794753	1.00[ASN][1000 genomes]
rs11795004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12003468	0.92[EUR][1000 genomes]
rs12005177	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12352336	1.00[ASN][1000 genomes]
rs12375859	1.00[ASN][1000 genomes]
rs12379480	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16919024	0.92[EUR][1000 genomes]
rs3199998	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41274951	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62579387	1.00[ASN][1000 genomes]
rs7028101	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029342	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036972	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037122	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037419	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7039994	0.92[EUR][1000 genomes]
rs7849019	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866700	0.90[EUR][1000 genomes]
rs7873560	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7874036	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103057600-103112600	Weak transcription	Fetal Brain Male	brain
2	chr9:103065000-103114200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:103066200-103112600	Weak transcription	Pancreas	Pancrea
4	chr9:103066200-103113200	Weak transcription	Spleen	Spleen
5	chr9:103066200-103113800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr9:103067600-103112400	Weak transcription	Small Intestine	intestine
7	chr9:103072200-103113800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr9:103074000-103113200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:103078400-103112200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:103082800-103111800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr9:103083800-103113800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr9:103088400-103112000	Weak transcription	Brain Germinal Matrix	brain
13	chr9:103088600-103112400	Weak transcription	Brain Angular Gyrus	brain
14	chr9:103088600-103113000	Weak transcription	Fetal Brain Female	brain
15	chr9:103088600-103114400	Weak transcription	Lung	lung
16	chr9:103088800-103112400	Weak transcription	Psoas Muscle	Psoas
17	chr9:103088800-103113400	Weak transcription	Fetal Intestine Small	intestine
18	chr9:103088800-103114400	Weak transcription	Gastric	stomach
19	chr9:103089400-103112800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr9:103090600-103111600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:103091200-103113200	Weak transcription	Liver	Liver
22	chr9:103092400-103112400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr9:103092400-103113800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr9:103092600-103113800	Weak transcription	Brain Hippocampus Middle	brain
25	chr9:103099000-103111800	Strong transcription	K562	blood
26	chr9:103100800-103112600	Weak transcription	Aorta	Aorta
27	chr9:103100800-103113800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:103101000-103113800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr9:103101400-103113200	Weak transcription	Fetal Stomach	stomach
30	chr9:103102000-103114000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr9:103104600-103113800	Weak transcription	Right Ventricle	heart
32	chr9:103104800-103111600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr9:103104800-103111600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr9:103104800-103112600	Weak transcription	Fetal Heart	heart
35	chr9:103105000-103111800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr9:103105000-103112600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr9:103105400-103114000	Weak transcription	Brain Substantia Nigra	brain
38	chr9:103107000-103113200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr9:103107200-103112400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr9:103107800-103111800	Strong transcription	NHEK	skin
41	chr9:103108000-103111800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr9:103108000-103112400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr9:103108000-103113800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr9:103108600-103112600	Weak transcription	Colon Smooth Muscle	Colon
45	chr9:103108600-103114000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr9:103109200-103112000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr9:103109200-103112400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:103109200-103112400	Weak transcription	NHLF	lung
49	chr9:103109200-103113200	Weak transcription	Fetal Lung	lung
50	chr9:103109200-103113400	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links