Variant report

Variant	rs1168968
Chromosome Location	chr2:96825363-96825364
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:96820286..96828646-chr2:96829192..96834775,11	K562	blood:
2	chr2:96820873..96826236-chr2:96872266..96875542,4	K562	blood:
3	chr2:96817307..96820123-chr2:96822215..96825688,4	K562	blood:
4	chr2:96824942..96826995-chr2:96828111..96830787,2	MCF-7	breast:
5	chr2:96825347..96828003-chr2:96929787..96932751,2	K562	blood:

Variant related genes	Relation type
ENSG00000135956	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000144021	Chromatin interaction
ENSG00000204685	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10183151	0.95[CEU][hapmap];0.83[YRI][hapmap];0.91[EUR][1000 genomes]
rs1030864	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11680950	0.95[CEU][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs11687113	0.92[GIH][hapmap]
rs1168965	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1168966	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs1168967	0.83[EUR][1000 genomes]
rs1168970	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1168972	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1168974	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1168975	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1168976	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11693248	0.83[EUR][1000 genomes]
rs13019188	0.80[CEU][hapmap]
rs1657502	0.82[CEU][hapmap];0.84[GIH][hapmap];0.80[EUR][1000 genomes]
rs1724121	0.85[EUR][1000 genomes]
rs1724125	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2140938	0.84[EUR][1000 genomes]
rs2229169	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2301707	1.00[CEU][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs2312955	1.00[ASW][hapmap];0.90[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2576437	0.84[EUR][1000 genomes]
rs2579519	0.81[GIH][hapmap]
rs2579549	0.85[EUR][1000 genomes]
rs2579550	0.86[EUR][1000 genomes]
rs2579552	0.87[EUR][1000 genomes]
rs2692893	0.86[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs2692894	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2692934	0.86[EUR][1000 genomes]
rs2692936	0.86[EUR][1000 genomes]
rs2692937	0.87[EUR][1000 genomes]
rs2917662	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2969490	0.86[CEU][hapmap];0.86[GIH][hapmap];0.84[EUR][1000 genomes]
rs2969491	0.95[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3111873	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3821051	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs4144055	0.91[GIH][hapmap];0.82[LWK][hapmap]
rs4426564	1.00[ASW][hapmap];0.90[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap]
rs4907299	0.90[CEU][hapmap];0.85[GIH][hapmap];0.90[EUR][1000 genomes]
rs58448550	0.83[EUR][1000 genomes]
rs749457	0.82[CEU][hapmap];0.84[GIH][hapmap];0.83[EUR][1000 genomes]
rs749459	0.82[CEU][hapmap];0.84[GIH][hapmap]
rs7561198	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7604842	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs772175	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap]
rs772178	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap]
rs810057	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs893173	0.82[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1840487	chr2:96582807-96836512	Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv874673	chr2:96647856-96825363	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv1825266	chr2:96704118-96830753	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1004129	chr2:96738585-96825363	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	nsv874675	chr2:96741944-96825363	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
9	nsv874676	chr2:96753149-96825363	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	esv1819594	chr2:96755038-96833480	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	nsv1008495	chr2:96755070-96825363	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
12	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
13	nsv1015000	chr2:96757107-96825363	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
14	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
15	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
16	nsv1007132	chr2:96767204-96829489	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1168968	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx
rs1168968	MRPL30	cis	parietal	SCAN
rs1168968	MGAT4A	cis	parietal	SCAN
rs1168968	FAHD2CP	cis	Muscle Skeletal	GTEx
rs1168968	FAHD2CP	cis	lung	GTEx
rs1168968	ADRA2B	cis	Thyroid	GTEx
rs1168968	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs1168968	ADRA2B	cis	Nerve Tibial	GTEx
rs1168968	CIAO1	cis	lymphoblastoid	seeQTL
rs1168968	GPAT2	cis	Adipose Subcutaneous	GTEx
rs1168968	GPAT2	cis	Muscle Skeletal	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96814400-96840000	Weak transcription	Right Atrium	heart
2	chr2:96818600-96827800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:96821000-96825600	Enhancers	Primary B cells from cord blood	blood
4	chr2:96821000-96825800	Enhancers	Primary B cells from peripheral blood	blood
5	chr2:96821000-96831800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:96821800-96825400	Enhancers	Spleen	Spleen
7	chr2:96821800-96825600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr2:96821800-96825600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:96821800-96825800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:96822200-96825800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:96823600-96827600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:96823800-96825600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr2:96823800-96826000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr2:96823800-96827000	Enhancers	Thymus	Thymus
15	chr2:96823800-96829200	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr2:96824000-96825800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:96824200-96825800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr2:96824200-96825800	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr2:96824200-96826000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr2:96824200-96827800	Weak transcription	Colonic Mucosa	Colon
21	chr2:96824200-96829200	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr2:96824200-96829200	Enhancers	Fetal Thymus	thymus
23	chr2:96824200-96829800	Enhancers	Primary T cells fromperipheralblood	blood
24	chr2:96824400-96825600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:96824600-96827600	Enhancers	GM12878-XiMat	blood
26	chr2:96824600-96830400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr2:96824800-96825400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:96824800-96827600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr2:96824800-96827600	Weak transcription	K562	blood
30	chr2:96825000-96825400	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr2:96825000-96825600	Enhancers	Dnd41	blood
32	chr2:96825000-96830200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr2:96825200-96825400	Bivalent Enhancer	HepG2	liver
34	chr2:96825200-96825600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:96825200-96827600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr2:96825200-96829200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links