Variant report

Variant	rs334701
Chromosome Location	chr1:61619056-61619057
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	chr1:61599982..61604281-chr1:61617367..61621050,4	K562	blood:
2	chr1:61605231..61608148-chr1:61617822..61620797,4	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs168022	0.85[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs334698	0.82[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes]
rs334699	0.87[ASW][hapmap];0.82[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes]
rs334700	0.82[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes]
rs334702	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs334703	0.87[ASW][hapmap];0.82[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes]
rs334704	0.87[ASW][hapmap];0.82[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes]
rs334705	1.00[CHB][hapmap];0.97[AFR][1000 genomes]
rs334706	0.82[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes]
rs334708	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs334709	0.82[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes]
rs334710	0.82[CEU][hapmap]
rs334711	0.85[CEU][hapmap]
rs334712	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs334713	0.82[CEU][hapmap];0.94[GIH][hapmap]
rs334716	0.82[CEU][hapmap];0.82[GIH][hapmap];0.87[MKK][hapmap]
rs334717	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs334720	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs334722	0.85[CEU][hapmap]
rs334723	0.82[CEU][hapmap];0.82[GIH][hapmap];0.80[LWK][hapmap];0.87[MKK][hapmap]
rs334724	0.88[EUR][1000 genomes]
rs334725	0.87[ASW][hapmap];0.82[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes]
rs334726	0.82[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes]
rs334727	0.96[AFR][1000 genomes]
rs334728	0.87[ASW][hapmap];0.82[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes]
rs334729	0.82[CEU][hapmap];0.87[AFR][1000 genomes]
rs334732	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs334733	0.87[GIH][hapmap]
rs334734	0.87[GIH][hapmap]
rs3748543	0.87[GIH][hapmap]
rs382704	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs395936	0.87[GIH][hapmap]
rs406412	0.87[GIH][hapmap]
rs4915728	0.85[EUR][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	nsv1008634	chr1:61613785-61671468	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs334701	HBG2	trans	brain	seeQTL
rs334701	HBG1	trans	brain	seeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:61606000-61649000	Weak transcription	Spleen	Spleen
2	chr1:61607600-61622200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:61607800-61622600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:61609600-61622800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:61610000-61621800	Weak transcription	Fetal Brain Male	brain
6	chr1:61610000-61623400	Weak transcription	Fetal Brain Female	brain
7	chr1:61610200-61622200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:61610200-61623200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:61612000-61635800	Weak transcription	Lung	lung
10	chr1:61612800-61626200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:61613400-61619800	Enhancers	Colon Smooth Muscle	Colon
12	chr1:61613800-61620600	Enhancers	Brain Hippocampus Middle	brain
13	chr1:61614800-61622000	Weak transcription	Ovary	ovary
14	chr1:61615200-61619600	Enhancers	Brain Anterior Caudate	brain
15	chr1:61615200-61620600	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr1:61615200-61621000	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr1:61615400-61619600	Enhancers	Fetal Heart	heart
18	chr1:61615400-61620000	Enhancers	Brain Substantia Nigra	brain
19	chr1:61615400-61635000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:61615400-61635600	Weak transcription	Hela-S3	cervix
21	chr1:61615600-61620600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:61615600-61622600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:61615600-61622600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:61615800-61621600	Weak transcription	Right Ventricle	heart
25	chr1:61615800-61621800	Weak transcription	K562	blood
26	chr1:61615800-61622400	Weak transcription	NHEK	skin
27	chr1:61616000-61622000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:61616000-61628000	Weak transcription	Gastric	stomach
29	chr1:61616600-61619600	Enhancers	Liver	Liver
30	chr1:61616800-61619400	Enhancers	Brain Cingulate Gyrus	brain
31	chr1:61616800-61622200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:61616800-61623200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:61617000-61619800	Enhancers	Rectal Smooth Muscle	rectum
34	chr1:61617000-61627800	Weak transcription	Esophagus	oesophagus
35	chr1:61617200-61619200	Enhancers	Fetal Kidney	kidney
36	chr1:61617200-61619200	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr1:61617200-61619400	Enhancers	Brain Angular Gyrus	brain
38	chr1:61617200-61619600	Enhancers	Fetal Lung	lung
39	chr1:61617200-61619600	Enhancers	Small Intestine	intestine
40	chr1:61617200-61619800	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr1:61617200-61620000	Enhancers	Fetal Intestine Small	intestine
42	chr1:61617200-61620600	Enhancers	Fetal Stomach	stomach
43	chr1:61617200-61620800	Enhancers	Fetal Intestine Large	intestine
44	chr1:61617400-61619200	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr1:61617400-61619400	Enhancers	Stomach Smooth Muscle	stomach
46	chr1:61617400-61619600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:61617800-61619200	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr1:61618000-61619800	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr1:61618000-61622600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:61618000-61622600	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links