Variant report

Variant	rs10414676
Chromosome Location	chr19:19243843-19243844
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	chr19:19243402-19244073	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr19:19243323-19244007	K562	blood:	n/a	n/a
3	POLR2A	chr19:19243572-19244042	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19241159..19242979-chr19:19243469..19246036,2	K562	blood:
2	chr19:19229446..19234006-chr19:19241302..19251526,15	K562	blood:
3	chr19:19169646..19176667-chr19:19241603..19249514,19	K562	blood:
4	chr19:19169646..19176603-chr19:19241603..19250623,23	K562	blood:

Variant related genes	Relation type
TMEM161A	TF binding region
ENSG00000181035	Chromatin interaction
ENSG00000064545	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1007483	1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs10405635	0.85[CHB][hapmap]
rs10410451	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10416783	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10417974	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs10423742	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1079543	0.85[CHB][hapmap]
rs10854005	0.82[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap]
rs11666340	0.82[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap]
rs11666627	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs11670204	0.81[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap]
rs12016	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs12976302	0.84[EUR][1000 genomes]
rs12979565	0.82[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap]
rs12979841	0.80[ASN][1000 genomes]
rs12985799	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs1859267	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2012318	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2040561	0.83[EUR][1000 genomes]
rs2040562	0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs2240094	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2269806	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2285851	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2872394	0.82[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3180770	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3826993	0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs4808906	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs4808907	0.82[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap]
rs4808913	0.82[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap]
rs4808916	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs4808924	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6511010	0.82[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap]
rs6511014	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs6511018	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs6511020	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs6511021	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248399	1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs7253244	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs7256648	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs7259609	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs7408301	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs757220	1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap]
rs757221	0.80[ASN][1000 genomes]
rs8104799	0.82[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap]
rs8110629	0.82[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap]
rs8111634	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs929215	0.82[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap]

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	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10414676	KIAA1683	cis	cerebellum	SCAN
rs10414676	MED26	cis	cerebellum	SCAN
rs10414676	NDUFA13	cis	parietal	SCAN
rs10414676	ZNF506	cis	parietal	SCAN
rs10414676	TMEM161A	cis	Muscle Skeletal	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19180600-19245600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr19:19180600-19248400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:19203800-19245600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr19:19217200-19247800	Weak transcription	Right Atrium	heart
5	chr19:19220400-19247800	Weak transcription	Psoas Muscle	Psoas
6	chr19:19222200-19248200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr19:19230800-19248400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr19:19231000-19245400	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr19:19231200-19248000	Weak transcription	Fetal Brain Male	brain
10	chr19:19231800-19245600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:19232200-19245200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr19:19232200-19245400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr19:19232600-19248000	Weak transcription	NHLF	lung
14	chr19:19233200-19245600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr19:19234600-19248000	Weak transcription	Primary B cells from cord blood	blood
16	chr19:19234800-19247800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:19235000-19247800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr19:19235200-19245600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr19:19241400-19245000	Weak transcription	K562	blood
20	chr19:19241400-19245200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr19:19242400-19244200	ZNF genes & repeats	Fetal Intestine Small	intestine
22	chr19:19242600-19244000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:19242600-19244200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr19:19242600-19244200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
25	chr19:19242600-19244200	ZNF genes & repeats	Fetal Intestine Large	intestine
26	chr19:19242600-19244200	ZNF genes & repeats	Fetal Stomach	stomach
27	chr19:19242800-19244000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
28	chr19:19242800-19244000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr19:19242800-19244000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:19242800-19244000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr19:19242800-19244000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
32	chr19:19242800-19244000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr19:19242800-19244000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
34	chr19:19242800-19244000	ZNF genes & repeats	Gastric	stomach
35	chr19:19242800-19244000	ZNF genes & repeats	Lung	lung
36	chr19:19242800-19244000	ZNF genes & repeats	Spleen	Spleen
37	chr19:19242800-19244200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
38	chr19:19242800-19244200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:19242800-19244200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr19:19242800-19244200	ZNF genes & repeats	Fetal Muscle Leg	muscle
41	chr19:19242800-19244200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
42	chr19:19243000-19244000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr19:19243000-19244200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
44	chr19:19243000-19244200	ZNF genes & repeats	Placenta	Placenta
45	chr19:19243200-19244000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr19:19243200-19244200	ZNF genes & repeats	A549	lung
47	chr19:19243200-19245200	Weak transcription	Fetal Kidney	kidney
48	chr19:19243200-19245600	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr19:19243200-19248000	Weak transcription	Osteobl	bone
50	chr19:19243400-19244200	Strong transcription	Dnd41	blood

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