Variant report

Variant	rs11627421
Chromosome Location	chr14:31167434-31167435
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:31158569..31160575-chr14:31165651..31167745,2	MCF-7	breast:
2	chr14:31164973..31167877-chr14:31174409..31177773,3	K562	blood:

Variant related genes	Relation type
ENSG00000092108	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10130830	0.81[CHB][hapmap]
rs10131166	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10136727	0.88[ASN][1000 genomes]
rs10141944	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10142331	0.81[CHB][hapmap]
rs10146357	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10147257	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10149966	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1113946	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs11156637	0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1123860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11622076	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11623154	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11625381	0.81[CHB][hapmap]
rs11628700	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11846293	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11846408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11846420	0.83[CHD][hapmap]
rs11851205	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12434151	0.81[CHB][hapmap]
rs12586678	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12882048	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12882931	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12888568	0.88[CEU][hapmap];0.95[MEX][hapmap]
rs12894186	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs142983	0.82[CEU][hapmap]
rs17096941	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]
rs17097023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17097130	0.84[AMR][1000 genomes]
rs17097160	0.88[CEU][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes]
rs172946	0.81[CHB][hapmap]
rs2038451	0.87[CEU][hapmap];0.80[AMR][1000 genomes]
rs2057284	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2070339	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs2070340	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2273520	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2273521	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2273522	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs229144	0.81[CHB][hapmap]
rs229150	0.80[CHB][hapmap];0.83[CHD][hapmap]
rs229152	0.81[CHB][hapmap]
rs229154	0.81[CHB][hapmap]
rs229155	0.83[CHD][hapmap]
rs229161	0.81[CHB][hapmap]
rs229164	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs229190	0.81[CHB][hapmap]
rs229209	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs229211	0.81[CHB][hapmap]
rs229244	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs230340	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs230351	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs230364	0.81[CHB][hapmap]
rs230366	0.81[CHB][hapmap]
rs2378780	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[MEX][hapmap];0.90[ASN][1000 genomes]
rs2378782	0.81[CHB][hapmap]
rs28567474	0.86[ASN][1000 genomes]
rs34935871	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35069045	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3736773	0.88[CEU][hapmap]
rs4430662	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61976741	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6571356	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6571357	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6571361	0.81[CHB][hapmap]
rs7141333	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7141624	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7144204	0.80[CHB][hapmap];0.85[CHD][hapmap]
rs7147530	0.81[CHB][hapmap]
rs7149113	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7153509	0.81[CHB][hapmap]
rs7154847	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs7493549	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs761956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8006314	0.81[CHB][hapmap]
rs8008094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8012325	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8012494	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs8013017	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8015536	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8018993	0.91[ASN][1000 genomes]
rs8019637	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9322864	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[ASN][1000 genomes]
rs9806111	0.81[CHB][hapmap];0.83[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	esv3364587	chr14:31167385-31167934	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11627421	SCFD1	cis	cerebellum	SCAN
rs11627421	SCFD1	cis	parietal	SCAN
rs11627421	G2E3	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:31113800-31205400	Weak transcription	Fetal Brain Male	brain
2	chr14:31115000-31167600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr14:31122800-31205200	Weak transcription	Brain Angular Gyrus	brain
4	chr14:31123000-31212000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr14:31123400-31216400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr14:31124400-31171400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr14:31125200-31170000	Weak transcription	Colon Smooth Muscle	Colon
8	chr14:31133800-31197400	Weak transcription	Aorta	Aorta
9	chr14:31153400-31169000	Weak transcription	Brain Hippocampus Middle	brain
10	chr14:31153600-31167600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr14:31153600-31174400	Weak transcription	NHDF-Ad	bronchial
12	chr14:31153600-31198800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr14:31153800-31187400	Weak transcription	Fetal Brain Female	brain
14	chr14:31160000-31206600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr14:31160000-31207200	Weak transcription	Right Ventricle	heart
16	chr14:31160200-31172800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr14:31160200-31176000	Strong transcription	HSMM	muscle
18	chr14:31160200-31178800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr14:31160400-31167600	Weak transcription	Fetal Stomach	stomach
20	chr14:31160400-31168200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr14:31160400-31205000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr14:31160600-31192400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr14:31160800-31167600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr14:31160800-31197400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr14:31160800-31198600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr14:31160800-31206200	Weak transcription	Small Intestine	intestine
27	chr14:31161000-31178600	Weak transcription	Stomach Mucosa	stomach
28	chr14:31161000-31180800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr14:31161000-31195600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr14:31161000-31195800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr14:31161600-31197000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr14:31161800-31199000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr14:31162000-31181000	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr14:31162000-31192000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr14:31162200-31192000	Weak transcription	A549	lung
36	chr14:31162200-31199200	Strong transcription	HepG2	liver
37	chr14:31162400-31204000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr14:31162600-31194000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr14:31162800-31183200	Weak transcription	Fetal Heart	heart
40	chr14:31163400-31179000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr14:31163600-31168200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr14:31163600-31168200	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr14:31163600-31168200	Strong transcription	Fetal Muscle Leg	muscle
44	chr14:31163600-31169400	Strong transcription	Primary B cells from cord blood	blood
45	chr14:31163600-31170400	Strong transcription	Liver	Liver
46	chr14:31163600-31171400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr14:31163600-31171600	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr14:31163600-31172000	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr14:31163600-31179400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr14:31163600-31180000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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