Variant report

Variant	rs17096941
Chromosome Location	chr14:31072622-31072623
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:31069776..31071443-chr14:31072053..31074757,2	K562	blood:
2	chr14:31070404..31072787-chr14:31077582..31080526,2	K562	blood:
3	chr14:31071248..31073927-chr14:31089916..31091588,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000092140	Chromatin interaction
ENSG00000092108	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10131166	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10141944	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10146357	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10147257	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[EUR][1000 genomes]
rs10149966	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1113946	0.88[CEU][hapmap];0.80[GIH][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes]
rs11156637	0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1123860	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11622076	0.89[EUR][1000 genomes]
rs11622786	0.80[AMR][1000 genomes]
rs11623154	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11627421	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11628700	0.94[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11846071	0.83[EUR][1000 genomes]
rs11846293	0.88[EUR][1000 genomes]
rs11846408	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[EUR][1000 genomes]
rs11851205	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12586678	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12882048	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12882931	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12888568	0.88[CEU][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes]
rs12894186	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs142983	0.82[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17097023	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17097160	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs2038451	0.87[CEU][hapmap]
rs2057284	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2070340	0.94[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs2273520	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2273521	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2273522	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs229164	0.82[AMR][1000 genomes]
rs229179	0.82[CHB][hapmap]
rs229184	0.82[CHB][hapmap]
rs229201	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs229237	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs229244	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.97[ASN][1000 genomes]
rs2378780	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs28567474	0.86[AMR][1000 genomes]
rs34935871	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35069045	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35389182	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3736773	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs3825740	0.84[AMR][1000 genomes]
rs4430662	0.94[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs447853	0.91[CHB][hapmap];0.85[CHD][hapmap];0.82[MEX][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs448175	0.81[CHB][hapmap];0.86[CHD][hapmap]
rs58049	0.82[CHB][hapmap]
rs59856095	0.84[AMR][1000 genomes]
rs61976741	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6571356	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6571357	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7141333	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7141624	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7149113	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7493549	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs761956	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8008094	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8009427	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8013017	0.89[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8015536	0.86[CHB][hapmap]
rs8019637	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9322864	0.86[CHB][hapmap];0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv564169	chr14:30819087-31541494	Strong transcription Genic enhancers ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1036419	chr14:30969616-31224226	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv901581	chr14:30978745-31585289	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv564171	chr14:31068090-31149630	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17096941	SCFD1	cis	multi-tissue	Pritchard
rs17096941	SCFD1	cis	cerebellum	SCAN
rs17096941	SCFD1	cis	parietal	SCAN
rs17096941	G2E3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:31043000-31079600	Weak transcription	Gastric	stomach
2	chr14:31043000-31090600	Weak transcription	Small Intestine	intestine
3	chr14:31047000-31079600	Weak transcription	Pancreas	Pancrea
4	chr14:31049600-31079600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr14:31050200-31079800	Weak transcription	Brain Angular Gyrus	brain
6	chr14:31051800-31079600	Weak transcription	Fetal Brain Male	brain
7	chr14:31052000-31077400	Weak transcription	Psoas Muscle	Psoas
8	chr14:31053600-31079800	Weak transcription	Brain Substantia Nigra	brain
9	chr14:31053800-31090600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr14:31054200-31090400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr14:31054800-31087200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr14:31055000-31086800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr14:31055600-31088000	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr14:31057400-31077600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr14:31057800-31079800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr14:31058400-31080000	Weak transcription	Fetal Heart	heart
17	chr14:31058800-31074800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr14:31059800-31080000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr14:31061600-31090400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr14:31064200-31078200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr14:31064400-31087800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr14:31064600-31073800	Strong transcription	Primary B cells from cord blood	blood
23	chr14:31064800-31078000	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr14:31064800-31086600	Strong transcription	Dnd41	blood
25	chr14:31064800-31087800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr14:31065000-31075000	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr14:31065400-31075000	Strong transcription	GM12878-XiMat	blood
28	chr14:31065600-31076800	Strong transcription	Primary B cells from peripheral blood	blood
29	chr14:31065600-31086600	Strong transcription	HepG2	liver
30	chr14:31065800-31083000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr14:31065800-31086800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr14:31065800-31087000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr14:31065800-31087600	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr14:31066000-31074400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr14:31066000-31074800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr14:31066000-31078200	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr14:31066000-31082400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr14:31066600-31074400	Strong transcription	Fetal Thymus	thymus
39	chr14:31066800-31073800	Strong transcription	HSMM	muscle
40	chr14:31066800-31074400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr14:31066800-31074400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr14:31066800-31074400	Strong transcription	Fetal Muscle Leg	muscle
43	chr14:31066800-31074600	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr14:31066800-31074600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr14:31066800-31074600	Strong transcription	Fetal Muscle Trunk	muscle
46	chr14:31066800-31075000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr14:31066800-31075000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr14:31066800-31075000	Strong transcription	Fetal Intestine Large	intestine
49	chr14:31067000-31075000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr14:31067200-31074600	Strong transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links