Variant report

Variant	rs9429830
Chromosome Location	chr1:210110537-210110538
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	REST	chr1:210110459-210111899	PFSK-1	brain:	n/a	chr1:210111591-210111604 chr1:210111694-210111707 chr1:210111126-210111144 chr1:210111586-210111599 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111676-210111689 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
2	REST	chr1:210110454-210112019	SK-N-SH	brain:	n/a	chr1:210111591-210111604 chr1:210111694-210111707 chr1:210111126-210111144 chr1:210111586-210111599 chr1:210111898-210111905 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111676-210111689 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
3	JUND	chr1:210110209-210112774	SK-N-SH	brain:	n/a	chr1:210111772-210111781
4	REST	chr1:210110524-210111516	HL-60	blood:	n/a	chr1:210111126-210111144 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
5	MXI1	chr1:210110276-210113314	SK-N-SH	brain:	n/a	n/a
6	REST	chr1:210110401-210111450	A549	lung:	n/a	chr1:210111126-210111144 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
7	REST	chr1:210110459-210111476	ECC-1	luminal epithelium:	n/a	chr1:210111126-210111144 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
8	REST	chr1:210110506-210111736	PFSK-1	brain:	n/a	chr1:210111591-210111604 chr1:210111694-210111707 chr1:210111126-210111144 chr1:210111586-210111599 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111676-210111689 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IRF6-1	chr1:210107873-210111294	NONHSAT009248

Variant related genes	Relation type
SYT14	TF binding region

Extended variants
information (count: 161 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:155)

rs_ID	r²[population]
rs1028325	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1040423	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10779516	0.88[EUR][1000 genomes]
rs10779517	0.87[EUR][1000 genomes]
rs10779518	0.87[EUR][1000 genomes]
rs10863799	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10863811	0.82[EUR][1000 genomes]
rs1099863	0.84[EUR][1000 genomes]
rs11119363	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11119369	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119370	0.93[EUR][1000 genomes]
rs11119374	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11119375	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11119376	0.85[EUR][1000 genomes]
rs11119378	0.83[ASN][1000 genomes]
rs11119382	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11119407	0.82[EUR][1000 genomes]
rs11119409	0.86[EUR][1000 genomes]
rs11119413	0.84[EUR][1000 genomes]
rs11119414	0.84[EUR][1000 genomes]
rs12025114	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12042135	0.86[EUR][1000 genomes]
rs12078439	0.86[EUR][1000 genomes]
rs12079815	0.90[EUR][1000 genomes]
rs12083466	0.94[EUR][1000 genomes]
rs12092530	0.95[EUR][1000 genomes]
rs126277	0.87[EUR][1000 genomes]
rs126278	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1334569	0.84[EUR][1000 genomes]
rs1387933	0.83[EUR][1000 genomes]
rs1387934	0.91[CHB][hapmap];0.87[JPT][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs170552	0.89[EUR][1000 genomes]
rs170553	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs170555	0.89[EUR][1000 genomes]
rs170557	0.84[EUR][1000 genomes]
rs170558	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs183450	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs189000	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs189001	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2046849	0.85[EUR][1000 genomes]
rs2142861	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2200970	0.84[EUR][1000 genomes]
rs2205987	0.84[EUR][1000 genomes]
rs2205988	0.87[EUR][1000 genomes]
rs2205989	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs227168	0.88[EUR][1000 genomes]
rs227169	0.83[EUR][1000 genomes]
rs227170	0.88[EUR][1000 genomes]
rs227171	0.88[EUR][1000 genomes]
rs227172	0.84[EUR][1000 genomes]
rs227173	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs227174	0.84[EUR][1000 genomes]
rs227175	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs227176	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs227177	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs227178	0.88[EUR][1000 genomes]
rs227179	0.83[EUR][1000 genomes]
rs227181	0.84[EUR][1000 genomes]
rs227182	0.84[EUR][1000 genomes]
rs227183	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs227184	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs227186	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs227187	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs227188	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs227189	0.82[EUR][1000 genomes]
rs227190	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs227191	0.84[EUR][1000 genomes]
rs227193	0.84[EUR][1000 genomes]
rs227195	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs227196	0.84[EUR][1000 genomes]
rs227197	0.84[EUR][1000 genomes]
rs227200	0.89[EUR][1000 genomes]
rs227201	0.83[EUR][1000 genomes]
rs227202	0.89[EUR][1000 genomes]
rs227203	0.83[EUR][1000 genomes]
rs227204	0.84[EUR][1000 genomes]
rs227205	0.84[EUR][1000 genomes]
rs227206	0.84[EUR][1000 genomes]
rs227207	0.88[EUR][1000 genomes]
rs227209	0.84[EUR][1000 genomes]
rs227211	0.83[EUR][1000 genomes]
rs227216	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs227217	0.83[EUR][1000 genomes]
rs227218	0.83[EUR][1000 genomes]
rs227219	0.83[EUR][1000 genomes]
rs227221	0.91[CHB][hapmap];0.87[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs227223	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs227224	0.84[EUR][1000 genomes]
rs227225	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs227226	0.83[EUR][1000 genomes]
rs227227	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs227228	0.84[EUR][1000 genomes]
rs227229	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs227230	0.84[EUR][1000 genomes]
rs227232	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2357212	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs2473073	0.80[EUR][1000 genomes]
rs2636373	0.91[EUR][1000 genomes]
rs2636376	0.84[EUR][1000 genomes]
rs2743889	0.84[EUR][1000 genomes]
rs2743891	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2884124	0.87[EUR][1000 genomes]
rs4282820	0.86[EUR][1000 genomes]
rs4454550	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4462143	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4844913	0.83[EUR][1000 genomes]
rs4844948	0.83[EUR][1000 genomes]
rs6540567	0.86[EUR][1000 genomes]
rs6540568	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6540569	0.96[CEU][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs6540570	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6540573	0.86[EUR][1000 genomes]
rs6657984	0.81[EUR][1000 genomes]
rs6662445	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6667057	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6678081	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6682334	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6682546	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6689456	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6702257	0.83[EUR][1000 genomes]
rs6702961	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs701947	0.96[CEU][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs701948	0.96[CEU][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs724054	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7513171	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7514257	0.84[EUR][1000 genomes]
rs7525980	0.84[EUR][1000 genomes]
rs7528647	0.96[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs7530426	0.87[EUR][1000 genomes]
rs7544033	0.92[EUR][1000 genomes]
rs7547709	0.84[EUR][1000 genomes]
rs7548989	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7549523	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7549696	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs846545	0.89[EUR][1000 genomes]
rs846548	0.89[EUR][1000 genomes]
rs846549	0.89[EUR][1000 genomes]
rs846550	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs846551	0.84[EUR][1000 genomes]
rs846552	0.84[EUR][1000 genomes]
rs846553	0.90[EUR][1000 genomes]
rs846554	0.84[EUR][1000 genomes]
rs846555	0.84[EUR][1000 genomes]
rs846556	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs846557	0.91[EUR][1000 genomes]
rs846559	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs860155	0.82[EUR][1000 genomes]
rs9429827	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9429829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9430020	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9430024	0.93[EUR][1000 genomes]
rs9430026	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9659395	0.80[EUR][1000 genomes]
rs9662387	0.93[EUR][1000 genomes]
rs986057	0.96[CEU][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873140	chr1:210068117-210335644	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv1825811	chr1:210082206-210135806	Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv1821002	chr1:210108473-210291476	ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv3438109	chr1:210110354-210112902	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210110200-210110600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:210110200-210112400	Active TSS	Brain Anterior Caudate	brain
3	chr1:210110200-210112800	Active TSS	Brain Angular Gyrus	brain
4	chr1:210110400-210110600	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr1:210110400-210110600	Enhancers	H1 Cell Line	embryonic stem cell
6	chr1:210110400-210110600	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr1:210110400-210110600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
8	chr1:210110400-210110600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr1:210110400-210110600	Enhancers	Brain Cingulate Gyrus	brain
10	chr1:210110400-210110600	Active TSS	Brain Hippocampus Middle	brain
11	chr1:210110400-210110600	Enhancers	HMEC	breast
12	chr1:210110400-210110800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:210110400-210111200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:210110400-210112400	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr1:210110400-210112800	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr1:210110400-210112800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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