Variant report

Variant	rs1169
Chromosome Location	chr3:121382204-121382205
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	chr3:121378844-121382265	K562	blood:	n/a	n/a
2	POLR2A	chr3:121381599-121382728	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:121381533..121383209-chr3:121385289..121388100,2	MCF-7	breast:
2	chr3:121374281..121376977-chr3:121381116..121385045,3	MCF-7	breast:
3	chr3:121380202..121382389-chr3:121387909..121390057,2	K562	blood:
4	chr3:121378883..121381780-chr3:121382077..121384890,2	K562	blood:

Variant related genes	Relation type
HCLS1	TF binding region
ENSG00000180353	Chromatin interaction
ENSG00000222057	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1127412	0.83[CHB][hapmap];0.81[CHD][hapmap]
rs1463736	0.83[CHB][hapmap];0.81[CHD][hapmap]
rs1574133	0.83[CHB][hapmap]
rs3732410	0.83[CHB][hapmap]
rs4048703	0.83[CHB][hapmap]
rs7153	0.83[CHB][hapmap];0.81[CHD][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	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv999335	chr3:121100283-121408766	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv998740	chr3:121289499-121390271	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1169	IQCB1	cis	cerebellum	SCAN
rs1169	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs1169	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs1169	ALG1L	cis	parietal	SCAN
rs1169	SLC15A2	cis	cerebellum	SCAN
rs1169	GOLGB1	cis	multi-tissue	Pritchard
rs1169	HCLS1	cis	multi-tissue	Pritchard
rs1169	SLC15A2	cis	parietal	SCAN
rs1169	IQCB1	cis	parietal	SCAN
rs1169	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121351000-121382800	Weak transcription	Small Intestine	intestine
2	chr3:121371000-121383600	Weak transcription	Hela-S3	cervix
3	chr3:121376400-121383000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:121377000-121383600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:121378000-121388400	Strong transcription	Fetal Stomach	stomach
6	chr3:121378400-121383200	Weak transcription	NH-A	brain
7	chr3:121379000-121384200	Enhancers	Fetal Heart	heart
8	chr3:121379400-121384600	Weak transcription	Fetal Kidney	kidney
9	chr3:121379400-121402400	Strong transcription	Fetal Intestine Large	intestine
10	chr3:121379800-121382400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:121379800-121382400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:121379800-121382400	Weak transcription	Ovary	ovary
13	chr3:121379800-121382400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:121379800-121382800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:121379800-121383000	Weak transcription	Esophagus	oesophagus
16	chr3:121379800-121384200	Genic enhancers	Fetal Muscle Leg	muscle
17	chr3:121380000-121382400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:121380000-121382800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:121380000-121402600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:121380200-121382600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:121380200-121382800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:121380200-121385200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr3:121380200-121386200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:121380200-121397000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:121380400-121382400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:121380400-121382600	Weak transcription	HUVEC	blood vessel
27	chr3:121380400-121384600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:121380400-121385400	Weak transcription	K562	blood
29	chr3:121380400-121386800	Strong transcription	Brain Anterior Caudate	brain
30	chr3:121380400-121396400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:121380400-121396800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:121380400-121402400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:121380400-121402800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:121380400-121406600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:121380600-121382400	Weak transcription	Primary B cells from cord blood	blood
36	chr3:121380600-121382400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr3:121380600-121382400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:121380600-121382800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr3:121380600-121384600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr3:121380600-121384800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr3:121380600-121384800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr3:121380600-121413800	Weak transcription	Stomach Mucosa	stomach
43	chr3:121380800-121382400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr3:121380800-121383000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:121380800-121383000	Weak transcription	NHEK	skin
46	chr3:121380800-121385000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr3:121380800-121386600	Strong transcription	HSMM	muscle
48	chr3:121380800-121389600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:121381000-121382400	Weak transcription	HMEC	breast
50	chr3:121381000-121383000	Weak transcription	Colon Smooth Muscle	Colon

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