Variant report

Variant	rs1946998
Chromosome Location	chr4:85566809-85566810
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 2 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1372971	0.80[MEX][hapmap]
rs4490450	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1946998	NKX6-1	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85518600-85574800	Weak transcription	Stomach Mucosa	stomach
2	chr4:85526800-85583000	Weak transcription	Gastric	stomach
3	chr4:85529400-85581600	Weak transcription	Ovary	ovary
4	chr4:85529600-85587600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:85532400-85571200	Weak transcription	Pancreas	Pancrea
6	chr4:85536800-85570200	Weak transcription	Fetal Stomach	stomach
7	chr4:85537200-85568600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:85538600-85568600	Weak transcription	Brain Anterior Caudate	brain
9	chr4:85544600-85568000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr4:85544600-85572400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr4:85545200-85576400	Weak transcription	Esophagus	oesophagus
12	chr4:85546600-85570400	Weak transcription	Small Intestine	intestine
13	chr4:85555200-85568800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr4:85556600-85570400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr4:85556600-85572200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:85556800-85570600	Weak transcription	Lung	lung
17	chr4:85556800-85570600	Weak transcription	NHEK	skin
18	chr4:85557600-85569200	Weak transcription	HMEC	breast
19	chr4:85559800-85567800	Weak transcription	Fetal Heart	heart
20	chr4:85560600-85567000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:85560600-85568600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr4:85560600-85568600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr4:85560600-85570600	Weak transcription	Left Ventricle	heart
24	chr4:85561400-85570200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr4:85562000-85567200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:85563000-85567400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr4:85563000-85568400	Weak transcription	Brain Hippocampus Middle	brain
28	chr4:85563400-85568000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr4:85563400-85570600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr4:85563600-85570600	Weak transcription	Fetal Intestine Small	intestine
31	chr4:85564200-85568600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr4:85564800-85567400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr4:85564800-85568600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr4:85564800-85568600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:85564800-85587800	Weak transcription	Fetal Kidney	kidney
36	chr4:85565000-85570600	Weak transcription	Placenta	Placenta
37	chr4:85565400-85568400	Weak transcription	Fetal Intestine Large	intestine
38	chr4:85565400-85568800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr4:85565400-85570600	Weak transcription	Aorta	Aorta
40	chr4:85565600-85568600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:85565600-85568800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr4:85566400-85567000	Strong transcription	Duodenum Mucosa	Duodenum
43	chr4:85566400-85570400	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr4:85566600-85567000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:85566600-85567800	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr4:85566800-85567200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links