Variant report

Variant	rs12121498
Chromosome Location	chr1:103380128-103380129
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1012281	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.92[ASN][1000 genomes]
rs10127706	0.92[ASN][1000 genomes]
rs10127873	0.92[ASN][1000 genomes]
rs10493986	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10874666	0.92[ASN][1000 genomes]
rs10874667	0.92[ASN][1000 genomes]
rs10874669	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs10874670	0.92[ASN][1000 genomes]
rs11164619	0.88[EUR][1000 genomes]
rs11164621	0.85[EUR][1000 genomes]
rs11164623	0.87[EUR][1000 genomes]
rs11164635	0.92[ASN][1000 genomes]
rs11164636	0.92[ASN][1000 genomes]
rs11164640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164643	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs11164655	0.92[ASN][1000 genomes]
rs11164663	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11586849	1.00[CHB][hapmap]
rs11801437	0.92[ASN][1000 genomes]
rs12062184	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs12064011	0.92[ASN][1000 genomes]
rs12064766	1.00[CHB][hapmap]
rs12078741	0.92[ASN][1000 genomes]
rs12084574	0.92[ASN][1000 genomes]
rs12084902	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs12116546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12117071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12118250	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12118259	1.00[ASN][1000 genomes]
rs12119468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120613	1.00[ASN][1000 genomes]
rs12120961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12121251	1.00[ASN][1000 genomes]
rs12121824	1.00[CHB][hapmap]
rs12121894	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs12121979	1.00[ASN][1000 genomes]
rs12123005	0.92[ASN][1000 genomes]
rs12124233	1.00[ASN][1000 genomes]
rs12124674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125432	0.92[ASN][1000 genomes]
rs12125550	1.00[ASN][1000 genomes]
rs12125551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126530	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12126635	1.00[ASN][1000 genomes]
rs12126868	0.80[CEU][hapmap];1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs12127007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127710	0.87[EUR][1000 genomes]
rs12128743	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12129927	0.85[ASN][1000 genomes]
rs12130285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133782	1.00[ASN][1000 genomes]
rs12134175	1.00[ASN][1000 genomes]
rs12135438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136421	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12140745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12141988	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12142137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142333	0.92[ASN][1000 genomes]
rs12145801	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12145872	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1337195	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1415363	1.00[CHD][hapmap]
rs1676487	1.00[ASN][1000 genomes]
rs17127270	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs2045819	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs2061706	0.81[EUR][1000 genomes]
rs2061707	0.87[EUR][1000 genomes]
rs2376260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2376261	0.92[ASN][1000 genomes]
rs2615975	0.92[ASN][1000 genomes]
rs2622834	1.00[ASN][1000 genomes]
rs2622858	0.92[ASN][1000 genomes]
rs28648038	1.00[ASN][1000 genomes]
rs2889331	0.87[EUR][1000 genomes]
rs3861742	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4391683	1.00[CHB][hapmap]
rs4908287	1.00[CHB][hapmap]
rs4908288	1.00[CHB][hapmap]
rs4908290	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6679803	0.92[ASN][1000 genomes]
rs6703720	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72983785	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73000234	0.87[EUR][1000 genomes]
rs74110526	0.92[ASN][1000 genomes]
rs7513552	1.00[CHB][hapmap]
rs7520435	1.00[CHB][hapmap]
rs7543082	0.80[CEU][hapmap];1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs7553464	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs992100	1.00[ASN][1000 genomes]
rs994027	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522922	chr1:103305021-103764640	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv870600	chr1:103336601-103548497	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv871809	chr1:103339272-103459537	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv871732	chr1:103339272-103466917	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv871475	chr1:103339272-103548497	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv462728	chr1:103342392-103455217	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv546930	chr1:103342392-103455217	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv870835	chr1:103349419-103409100	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv871533	chr1:103349419-103412000	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv870487	chr1:103349419-103466917	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv871019	chr1:103350903-103466917	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv870601	chr1:103352451-103409100	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv870881	chr1:103352451-103416690	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv870952	chr1:103352451-103432687	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv871807	chr1:103352451-103450196	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv871335	chr1:103352451-103459537	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv870644	chr1:103352451-103466917	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv871741	chr1:103352451-103517428	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv871078	chr1:103352451-103548497	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv462739	chr1:103354138-103402184	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv546931	chr1:103354138-103402184	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv871194	chr1:103354138-103416690	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv871970	chr1:103354138-103450196	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	nsv871494	chr1:103354138-103466917	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	nsv462750	chr1:103355765-103380128	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
26	nsv546932	chr1:103355765-103380128	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
27	nsv462761	chr1:103356168-103455217	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
28	nsv546933	chr1:103356168-103455217	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	nsv870607	chr1:103362909-103528128	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12121498	RAB4A	trans	lymphoblastoid	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:103345600-103385600	Weak transcription	HSMMtube	muscle
2	chr1:103350400-103380200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:103352600-103403200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:103363600-103384400	Weak transcription	HSMM	muscle
5	chr1:103363800-103385400	Weak transcription	NH-A	brain
6	chr1:103369600-103498600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:103371200-103385000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:103376000-103380400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:103376000-103385800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:103376200-103381600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:103376200-103382200	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:103376400-103381400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:103377400-103380400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:103378000-103380200	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:103378400-103380400	Strong transcription	Osteobl	bone
16	chr1:103378600-103381200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:103378800-103400000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:103380000-103399000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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