Variant report

Variant	rs12135774
Chromosome Location	chr1:10386506-10386507
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10362138..10364567-chr1:10385021..10386678,2	K562	blood:
2	chr1:10386481..10388666-chr1:10391684..10394464,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10864454	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11121542	0.98[EUR][1000 genomes]
rs11121548	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11121556	1.00[CHB][hapmap]
rs12119075	1.00[CHB][hapmap]
rs12120465	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12120499	0.88[EUR][1000 genomes]
rs12125492	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs12135219	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12137527	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12139158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12141192	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[LWK][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12142043	0.93[EUR][1000 genomes]
rs17396340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs17397129	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs17400878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs17401588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs3762289	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4240912	0.93[EUR][1000 genomes]
rs4240913	0.93[EUR][1000 genomes]
rs4846204	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs4846214	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4846215	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4846217	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58036267	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61383940	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6541092	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6670157	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6679596	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6693965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6694081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6702280	0.84[EUR][1000 genomes]
rs6703602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7525661	0.93[EUR][1000 genomes]
rs997482	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv545381	chr1:10296452-10423988	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv437200	chr1:10366487-10387704	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv437201	chr1:10370312-10387704	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers 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	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12135774	KIF1B	cis	lymphoblastoid	seeQTL
rs12135774	KIF1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10357600-10397000	Weak transcription	Fetal Thymus	thymus
2	chr1:10358800-10407000	Weak transcription	Primary B cells from cord blood	blood
3	chr1:10364200-10394600	Weak transcription	Dnd41	blood
4	chr1:10364600-10431000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:10365200-10398400	Weak transcription	Fetal Heart	heart
6	chr1:10365800-10394800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:10370200-10393800	Weak transcription	Right Atrium	heart
8	chr1:10378200-10397200	Weak transcription	GM12878-XiMat	blood
9	chr1:10378800-10388200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr1:10378800-10395200	Weak transcription	Thymus	Thymus
11	chr1:10379400-10397200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:10379800-10387200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr1:10379800-10399400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:10380000-10388800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr1:10380200-10399800	Weak transcription	Stomach Mucosa	stomach
16	chr1:10380200-10404800	Weak transcription	Psoas Muscle	Psoas
17	chr1:10380400-10386800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:10380400-10399600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:10380400-10436600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:10380600-10394400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:10380600-10401000	Weak transcription	A549	lung
22	chr1:10380600-10426400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:10380800-10394200	Weak transcription	K562	blood
24	chr1:10381000-10389800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:10381000-10436400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:10381600-10386600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:10381600-10386800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:10381600-10387200	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr1:10381600-10388000	Strong transcription	Brain Hippocampus Middle	brain
30	chr1:10381600-10388200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:10381600-10388600	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr1:10381600-10389000	Strong transcription	Brain Germinal Matrix	brain
33	chr1:10381600-10389200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:10381600-10391400	Strong transcription	Adipose Nuclei	Adipose
35	chr1:10381600-10392000	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:10381600-10392200	Strong transcription	Fetal Brain Female	brain
37	chr1:10381800-10386800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:10381800-10386800	Strong transcription	Fetal Intestine Large	intestine
39	chr1:10381800-10386800	Strong transcription	Left Ventricle	heart
40	chr1:10381800-10386800	Strong transcription	Stomach Smooth Muscle	stomach
41	chr1:10381800-10387000	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:10381800-10387200	Strong transcription	HepG2	liver
43	chr1:10381800-10387800	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr1:10381800-10388200	Strong transcription	Fetal Muscle Leg	muscle
45	chr1:10381800-10388200	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr1:10381800-10388400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:10381800-10388800	Strong transcription	Fetal Muscle Trunk	muscle
48	chr1:10381800-10389000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr1:10381800-10389400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:10381800-10389600	Strong transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links