Variant report

Variant	rs4808176
Chromosome Location	chr19:19133414-19133415
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19093006..19095343-chr19:19131973..19134830,2	K562	blood:
2	chr19:19131657..19133627-chr19:19143750..19145412,2	K562	blood:
3	chr19:19131657..19140875-chr19:19141068..19145619,15	K562	blood:
4	chr19:19132088..19135001-chr19:19135868..19138167,2	MCF-7	breast:
5	chr19:19125900..19131875-chr19:19132072..19136394,7	K562	blood:

Variant related genes	Relation type
ENSG00000105676	Chromatin interaction
ENSG00000064607	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10403272	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10410399	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[GIH][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11085249	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11671696	0.95[ASN][1000 genomes]
rs12978990	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2013585	0.87[EUR][1000 genomes]
rs2013813	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269807	0.82[AMR][1000 genomes]
rs2269869	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2285851	0.81[CEU][hapmap]
rs3787041	0.85[JPT][hapmap]
rs4808172	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4808177	0.82[AMR][1000 genomes]
rs4808182	1.00[AFR][1000 genomes]
rs4808895	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808900	0.95[ASN][1000 genomes]
rs4808916	0.85[JPT][hapmap]
rs4808917	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6511019	1.00[ASW][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs7252615	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs757222	1.00[AFR][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	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv1059305	chr19:19131310-19209999	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4808176	TSSK6	cis	cerebellum	SCAN
rs4808176	ZNF14	cis	parietal	SCAN
rs4808176	SFRS14	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19101200-19140200	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr19:19101400-19142000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr19:19106800-19143000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:19107200-19142600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:19107600-19142600	Strong transcription	Fetal Stomach	stomach
6	chr19:19108000-19142000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:19108000-19142800	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr19:19108200-19142600	Weak transcription	Right Atrium	heart
9	chr19:19108600-19142200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr19:19108600-19142800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr19:19109000-19141800	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr19:19109400-19142400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:19110600-19142400	Strong transcription	Fetal Muscle Trunk	muscle
14	chr19:19111000-19133600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr19:19123600-19133600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr19:19126400-19143400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr19:19126600-19137600	Strong transcription	Fetal Muscle Leg	muscle
18	chr19:19126800-19142600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:19127800-19135200	Weak transcription	Psoas Muscle	Psoas
20	chr19:19128000-19142200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr19:19128000-19142800	Strong transcription	Fetal Intestine Small	intestine
22	chr19:19128000-19142800	Weak transcription	Stomach Mucosa	stomach
23	chr19:19128400-19136200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr19:19130200-19135000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr19:19130200-19136200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr19:19130200-19141800	Weak transcription	Fetal Heart	heart
27	chr19:19131200-19142000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:19131200-19142800	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr19:19131400-19133600	Strong transcription	Fetal Brain Female	brain
30	chr19:19131400-19133800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr19:19131400-19139800	Strong transcription	K562	blood
32	chr19:19131400-19140200	Strong transcription	Adipose Nuclei	Adipose
33	chr19:19131400-19142400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr19:19132000-19134000	Genic enhancers	Dnd41	blood
35	chr19:19132000-19140800	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr19:19132000-19142000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr19:19132200-19133600	Strong transcription	NHEK	skin
38	chr19:19132200-19141200	Strong transcription	Stomach Smooth Muscle	stomach
39	chr19:19132200-19141800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr19:19132200-19142000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:19132400-19133600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr19:19132400-19133600	Weak transcription	HUVEC	blood vessel
43	chr19:19132400-19133800	Strong transcription	Duodenum Mucosa	Duodenum
44	chr19:19132400-19134400	Genic enhancers	Brain Angular Gyrus	brain
45	chr19:19132400-19139600	Strong transcription	Colon Smooth Muscle	Colon
46	chr19:19132400-19142400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr19:19132600-19133600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr19:19132600-19133600	Strong transcription	Fetal Kidney	kidney
49	chr19:19132600-19134800	Strong transcription	Pancreas	Pancrea
50	chr19:19132600-19138400	Strong transcription	Primary B cells from cord blood	blood

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