Variant report

Variant	rs41274646
Chromosome Location	chr9:101981229-101981230
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:101980127-101981375	GM12878	blood:	n/a	n/a
2	POLR2A	chr9:101979154-101981293	HepG2	liver:	n/a	n/a
3	POLR2A	chr9:101980965-101981329	GM12891	blood:	n/a	n/a
4	POLR2A	chr9:101980191-101981365	GM12878	blood:	n/a	n/a
5	POLR2A	chr9:101981141-101981249	HepG2	liver:	n/a	n/a
6	POLR2A	chr9:101977385-101982443	HepG2	liver:	n/a	n/a
7	POLR2A	chr9:101981111-101981353	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:101954549..101958495-chr9:101980489..101982138,3	MCF-7	breast:
2	chr9:101980463..101982045-chr9:102014372..102016907,2	K562	blood:

Variant related genes	Relation type
SEC61B	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10819642	0.89[EUR][1000 genomes]
rs11545137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11788822	0.86[AMR][1000 genomes]
rs12002203	0.87[ASN][1000 genomes]
rs12003123	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12005715	0.87[ASN][1000 genomes]
rs16918376	0.87[ASN][1000 genomes]
rs17725470	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17725597	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17725608	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17725644	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17725679	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs17725720	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs17787503	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17787533	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17787606	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28608552	0.87[ASN][1000 genomes]
rs35626507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780616	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41274648	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4265241	0.87[ASN][1000 genomes]
rs4554535	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs55676416	0.87[ASN][1000 genomes]
rs58644416	0.87[ASN][1000 genomes]
rs73653775	0.87[ASN][1000 genomes]
rs7857426	1.00[ASN][1000 genomes]
rs7863354	0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831666	chr9:101874985-102018690	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101964000-101982000	Weak transcription	Brain Substantia Nigra	brain
2	chr9:101964200-101981800	Weak transcription	Brain Hippocampus Middle	brain
3	chr9:101973200-101982000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr9:101974400-101983200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:101974600-101983400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:101976200-101981800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr9:101976600-101981400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:101976800-101981600	Weak transcription	NH-A	brain
9	chr9:101976800-101981800	Weak transcription	Fetal Brain Male	brain
10	chr9:101976800-101981800	Strong transcription	Fetal Muscle Leg	muscle
11	chr9:101976800-101982200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:101977000-101981800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr9:101977000-101983000	Weak transcription	Colonic Mucosa	Colon
14	chr9:101977400-101982200	Strong transcription	Fetal Thymus	thymus
15	chr9:101977600-101981400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr9:101977600-101981800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:101977600-101981800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:101977600-101982000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:101977600-101982400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:101977600-101982600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:101978000-101982000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr9:101978200-101981800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr9:101978400-101981600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr9:101978400-101982200	Strong transcription	HSMM	muscle
25	chr9:101978400-101983000	Weak transcription	Fetal Kidney	kidney
26	chr9:101978600-101982000	Weak transcription	Colon Smooth Muscle	Colon
27	chr9:101978600-101983200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr9:101978800-101982200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:101978800-101983000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr9:101979000-101981400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr9:101979200-101981800	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr9:101979400-101981400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr9:101979400-101982000	Weak transcription	Fetal Lung	lung
34	chr9:101979600-101981600	Strong transcription	K562	blood
35	chr9:101979600-101981800	Weak transcription	Stomach Mucosa	stomach
36	chr9:101979600-101982000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr9:101980000-101981400	Strong transcription	Hela-S3	cervix
38	chr9:101980200-101981400	Strong transcription	Adipose Nuclei	Adipose
39	chr9:101980200-101981400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr9:101980200-101981400	Strong transcription	Fetal Intestine Small	intestine
41	chr9:101980200-101981400	Strong transcription	Placenta	Placenta
42	chr9:101980200-101981400	Genic enhancers	Left Ventricle	heart
43	chr9:101980200-101981400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
44	chr9:101980200-101981400	Strong transcription	NHLF	lung
45	chr9:101980200-101981600	Strong transcription	NHEK	skin
46	chr9:101980200-101982000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
47	chr9:101980200-101982200	Weak transcription	Fetal Heart	heart
48	chr9:101980400-101981400	Genic enhancers	Ovary	ovary
49	chr9:101980400-101981600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr9:101980400-101981600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood

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