Variant report

Variant	rs11164109
Chromosome Location	chr2:97300833-97300834
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:97300809-97300859	MCF10A-Er-Src	breast:	n/a
2	chr2:97300809-97300859	SK-N-MC	brain:	n/a
3	chr2:97300809-97300859	HCF	heart:	n/a
4	chr2:97300809-97300859	HUVEC	blood vessel:	n/a
5	chr2:97300809-97300859	Jurkat	blood:	n/a
6	chr2:97300809-97300859	NHDF-neo	bronchial:	n/a
7	chr2:97300809-97300859	GM12892	blood:	n/a
8	chr2:97300809-97300859	HEEpiC	esophagus:	n/a
9	chr2:97300809-97300859	RPTEC	kidney:	n/a
10	chr2:97300809-97300859	HRCEpiC	kidney:	n/a
11	chr2:97300809-97300859	HCT-116	colon:	n/a
12	chr2:97300809-97300859	LNCaP	prostate:	n/a
13	chr2:97300809-97300859	AG04449	skin:	fetal
14	chr2:97300809-97300859	ECC-1	luminal epithelium:	n/a
15	chr2:97300809-97300859	SAEC	small airway:	n/a
16	chr2:97300809-97300859	GM12878	blood:	n/a
17	chr2:97300809-97300859	HCPEpiC	choroid plexus:	n/a
18	chr2:97300809-97300859	HEK293	kidney:	embryo
19	chr2:97300809-97300859	Caco-2	colon:	n/a
20	chr2:97300809-97300859	AG10803	skin:	n/a
21	chr2:97300809-97300859	HRE	kidney:	n/a
22	chr2:97300809-97300859	HCM	heart:	n/a
23	chr2:97300809-97300859	NT2-D1	testis:	n/a
24	chr2:97300809-97300859	MCF-7	breast:	n/a
25	chr2:97300809-97300859	AG04450	lung:	fetal
26	chr2:97300809-97300859	HNPCEpiC	eye:	n/a
27	chr2:97300809-97300859	NH-A	brain:	n/a
28	chr2:97300809-97300859	HIPEpiC	eye:	n/a
29	chr2:97300809-97300859	K562	blood:	n/a
30	chr2:97300809-97300859	HAEpiC	amniotic membrane:	n/a
31	chr2:97300809-97300859	GM12891	blood:	n/a
32	chr2:97300809-97300859	SK-N-SH	brain:	n/a
33	chr2:97300809-97300859	T-47D	breast:	n/a
34	chr2:97300809-97300859	PFSK-1	brain:	n/a
35	chr2:97300809-97300859	Hela-S3	cervix:	n/a
36	chr2:97300809-97300859	NB4	blood:	n/a
37	chr2:97300809-97300859	CMK	blood:	n/a
38	chr2:97300809-97300859	H1-hESC	embryonic stem cell:	embryo
39	chr2:97300809-97300859	IMR90	lung:	fetal
40	chr2:97300809-97300859	A549	lung:	n/a
41	chr2:97300809-97300859	HMEC	breast:	n/a
42	chr2:97300809-97300859	AG09309	skin:	n/a
43	chr2:97300809-97300859	GM19239	blood:	n/a
44	chr2:97300809-97300859	SK-N-SH_RA	brain:	n/a
45	chr2:97300809-97300859	U87	brain:	n/a
46	chr2:97300809-97300859	BE2_C	brain:	n/a
47	chr2:97300809-97300859	ProgFib	skin:	n/a
48	chr2:97300809-97300859	HRPEpiC	eye:	n/a
49	chr2:97300809-97300859	HL-60	blood:	n/a
50	chr2:97300809-97300859	Hepatocyte	liver:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:97299733..97305587-chr2:97422203..97428186,8	K562	blood:
2	chr2:97300473..97305040-chr2:97425563..97430425,4	MCF-7	breast:
3	chr2:97280954..97282617-chr2:97300423..97302279,2	MCF-7	breast:
4	chr2:97295918..97298197-chr2:97299685..97302124,2	MCF-7	breast:
5	chr2:97299005..97302154-chr2:97360237..97363363,3	K562	blood:
6	chr2:97299733..97305587-chr2:97425305..97429139,7	K562	blood:
7	chr2:97299848..97302209-chr2:97302318..97304171,2	MCF-7	breast:

No data

Variant related genes	Relation type
KANSL3	CpG island
ENSG00000114982	Chromatin interaction
ENSG00000249715	Chromatin interaction
ENSG00000158158	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10460601	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11677722	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11678174	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11682934	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11691670	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12469420	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12471390	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12477059	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2278563	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4907237	0.81[EUR][1000 genomes]
rs4907240	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4907241	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4907242	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4907246	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62154845	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62156200	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66727130	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6747149	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6749159	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6759099	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7575254	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7580048	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7600903	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	esv3460902	chr2:97138421-97459342	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	esv3460903	chr2:97138421-97459342	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	nsv999871	chr2:97157196-97407711	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv535829	chr2:97157196-97407711	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv469775	chr2:97240926-97412491	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv482586	chr2:97240926-97412491	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv834306	chr2:97241115-97412938	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11164109	CIAO1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97258200-97302800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:97261200-97301600	Strong transcription	Fetal Thymus	thymus
3	chr2:97285400-97302400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:97285800-97302800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:97288400-97301800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:97289600-97301400	Strong transcription	Fetal Intestine Large	intestine
7	chr2:97291000-97302000	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:97292200-97301400	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr2:97292200-97301800	Weak transcription	Stomach Mucosa	stomach
10	chr2:97292200-97302400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:97292200-97302400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr2:97292200-97302600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:97292400-97302200	Strong transcription	Fetal Muscle Leg	muscle
14	chr2:97292600-97301000	Strong transcription	Primary B cells from peripheral blood	blood
15	chr2:97292600-97301400	Strong transcription	Fetal Muscle Trunk	muscle
16	chr2:97292600-97301400	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr2:97292800-97301200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:97292800-97302000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:97293000-97301200	Strong transcription	Fetal Stomach	stomach
20	chr2:97293200-97301000	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr2:97293400-97302000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:97293600-97301200	Strong transcription	Primary B cells from cord blood	blood
23	chr2:97294800-97302800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:97296000-97302600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:97296400-97301000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:97296800-97301000	Strong transcription	Fetal Intestine Small	intestine
27	chr2:97297000-97301000	Strong transcription	Liver	Liver
28	chr2:97297200-97301000	Weak transcription	Brain Substantia Nigra	brain
29	chr2:97297200-97301400	Weak transcription	Spleen	Spleen
30	chr2:97297200-97301600	Weak transcription	Fetal Brain Male	brain
31	chr2:97297200-97301800	Weak transcription	HUVEC	blood vessel
32	chr2:97297200-97302000	Weak transcription	Brain Angular Gyrus	brain
33	chr2:97297200-97302600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr2:97297200-97302800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:97297400-97302000	Weak transcription	Colonic Mucosa	Colon
36	chr2:97297400-97302000	Weak transcription	HMEC	breast
37	chr2:97297600-97301200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:97297600-97302200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr2:97297800-97302800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr2:97298200-97301000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr2:97298200-97301200	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr2:97298200-97301600	Weak transcription	Pancreas	Pancrea
43	chr2:97298200-97302000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:97298200-97302600	Weak transcription	Gastric	stomach
45	chr2:97298400-97301000	Strong transcription	HepG2	liver
46	chr2:97298400-97301200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr2:97298400-97301400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:97298400-97302000	Weak transcription	Fetal Brain Female	brain
49	chr2:97298400-97302000	Weak transcription	Right Atrium	heart
50	chr2:97298400-97302000	Weak transcription	Small Intestine	intestine

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