Variant report

Variant	rs1430166
Chromosome Location	chr2:134089004-134089005
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	chr2:134088957-134089420	H1-neurons	neurons:	n/a	n/a
2	SIN3AK20	chr2:134088933-134089885	MCF-7	breast:	n/a	n/a
3	SRF	chr2:134088936-134089548	MCF-7	breast:	n/a	chr2:134089195-134089213
4	POLR2A	chr2:134088942-134089619	H1-neurons	neurons:	n/a	n/a
5	SRF	chr2:134088962-134089583	MCF-7	breast:	n/a	chr2:134089195-134089213
6	ZNF263	chr2:134088908-134089667	HEK293-T-REx	kidney:	n/a	n/a
7	REST	chr2:134088783-134089777	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:134088192..134090911-chr2:134099454..134100959,2	MCF-7	breast:
2	chr2:134088967..134089889-chr2:134250249..134251166,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-579P	TF binding region

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10165601	0.93[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10171473	0.86[ASN][1000 genomes]
rs10175744	0.93[CEU][hapmap];0.86[CHB][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10180047	0.84[ASW][hapmap];0.93[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10182402	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10182656	0.85[ASN][1000 genomes]
rs10184630	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10191826	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10193087	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10193730	0.86[ASN][1000 genomes]
rs10196395	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10204436	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10204527	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10206474	0.86[ASN][1000 genomes]
rs10469580	0.88[ASN][1000 genomes]
rs10928450	0.82[ASN][1000 genomes]
rs10928451	0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11884182	0.81[ASN][1000 genomes]
rs11890293	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11898252	0.85[ASN][1000 genomes]
rs12327930	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12328723	0.93[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12328976	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12619465	0.95[EUR][1000 genomes]
rs13392963	0.86[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13396831	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13396930	0.83[ASN][1000 genomes]
rs13400561	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13400743	1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13406057	0.80[CEU][hapmap];0.88[ASN][1000 genomes]
rs13406354	0.93[CEU][hapmap];0.86[CHB][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13407205	0.81[CEU][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13407503	0.81[CEU][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs13408835	0.85[ASN][1000 genomes]
rs13409478	1.00[CEU][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs13411233	0.93[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13412956	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13414823	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13417230	0.80[TSI][hapmap]
rs13421761	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13426157	0.82[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs13426681	0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs13432602	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1346776	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1369509	0.81[TSI][hapmap]
rs1369510	0.86[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1430165	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1430167	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1430168	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1435554	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1435556	0.93[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1435563	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1435564	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1435565	0.93[CEU][hapmap];0.86[CHB][hapmap];0.81[YRI][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1435566	0.93[CEU][hapmap];0.86[CHB][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1561018	1.00[JPT][hapmap];0.90[TSI][hapmap];0.85[ASN][1000 genomes]
rs16824301	0.82[ASN][1000 genomes]
rs16824303	0.82[ASN][1000 genomes]
rs16824511	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs16824573	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17745593	0.87[TSI][hapmap];0.85[ASN][1000 genomes]
rs17745851	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17802295	0.93[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1898008	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2115864	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2289075	0.87[TSI][hapmap];0.89[ASN][1000 genomes]
rs2304404	0.87[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28445548	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4588241	0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs55788182	0.92[ASN][1000 genomes]
rs56212259	0.92[EUR][1000 genomes]
rs56410092	0.82[ASN][1000 genomes]
rs57942569	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58035542	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58489491	0.88[ASN][1000 genomes]
rs59037048	0.89[EUR][1000 genomes]
rs62177662	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62177669	0.85[ASN][1000 genomes]
rs62177672	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62180011	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62180012	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62180016	0.94[ASN][1000 genomes]
rs62180017	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6724854	0.81[AFR][1000 genomes]
rs6724865	0.85[AFR][1000 genomes]
rs7573164	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9287426	0.93[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9808364	0.81[ASN][1000 genomes]
rs9808392	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs990476	1.00[JPT][hapmap];0.86[ASN][1000 genomes]

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	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1002488	chr2:133890159-134275312	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv535928	chr2:133890159-134275312	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv3375790	chr2:133906915-134222833	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv834384	chr2:134005229-134188648	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1014718	chr2:134067133-134151633	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv522324	chr2:134085665-134174032	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134070400-134094600	Weak transcription	NHEK	skin
2	chr2:134083400-134090400	Weak transcription	NHDF-Ad	bronchial
3	chr2:134084800-134092200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr2:134085000-134092000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:134085000-134093000	Weak transcription	Brain Substantia Nigra	brain
6	chr2:134086200-134092200	Weak transcription	Brain Anterior Caudate	brain
7	chr2:134087000-134090400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:134087200-134090800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:134087400-134103800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:134087600-134095600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:134088400-134089400	Enhancers	A549	lung
12	chr2:134088400-134090000	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr2:134088800-134093800	Enhancers	Hela-S3	cervix
14	chr2:134089000-134089400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:134089000-134089400	Enhancers	Right Atrium	heart
16	chr2:134089000-134089600	Enhancers	Left Ventricle	heart

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