Variant report

Variant	rs12476554
Chromosome Location	chr2:10727747-10727748
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:10726638..10728292-chr2:10728374..10731132,2	MCF-7	breast:
2	chr2:10724831..10728793-chr2:10731457..10735556,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234818	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10084172	0.84[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10166765	0.91[ASN][1000 genomes]
rs10167779	0.90[ASN][1000 genomes]
rs10168351	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10168852	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10174605	0.91[ASN][1000 genomes]
rs10175555	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs10175884	0.89[ASN][1000 genomes]
rs10177062	0.88[ASN][1000 genomes]
rs10178587	0.91[AFR][1000 genomes]
rs10178751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179854	0.81[ASN][1000 genomes]
rs10182589	0.91[ASN][1000 genomes]
rs10183359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10183883	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10186984	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187659	0.87[ASN][1000 genomes]
rs10188373	0.89[ASN][1000 genomes]
rs10190673	0.89[ASN][1000 genomes]
rs10190774	0.89[ASN][1000 genomes]
rs10198971	0.89[ASN][1000 genomes]
rs10199635	0.83[ASN][1000 genomes]
rs10199831	0.91[ASN][1000 genomes]
rs10202370	0.90[ASN][1000 genomes]
rs10207885	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208103	0.91[ASN][1000 genomes]
rs10211190	0.91[ASN][1000 genomes]
rs10803724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10803725	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10929676	0.85[LWK][hapmap]
rs10929677	0.89[ASN][1000 genomes]
rs10929678	0.91[ASN][1000 genomes]
rs10929679	0.91[ASN][1000 genomes]
rs10929680	0.91[ASN][1000 genomes]
rs10929681	0.84[CHB][hapmap];0.91[ASN][1000 genomes]
rs10929683	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929684	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929685	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680664	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11684537	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12104950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12329184	0.91[ASN][1000 genomes]
rs12473787	0.87[ASN][1000 genomes]
rs12473957	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[ASN][1000 genomes]
rs12475662	0.88[ASN][1000 genomes]
rs12613769	0.90[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12618726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621977	0.91[ASN][1000 genomes]
rs12622053	0.91[ASN][1000 genomes]
rs12690510	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12692412	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs12692414	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12692420	0.88[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs12995465	0.89[ASN][1000 genomes]
rs12996735	0.89[ASN][1000 genomes]
rs13009015	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13027316	0.90[ASN][1000 genomes]
rs13407040	0.88[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs13424648	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13425171	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13427815	0.86[ASN][1000 genomes]
rs13430911	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1861299	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1861300	0.96[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2024432	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024433	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2160258	0.89[ASN][1000 genomes]
rs2884232	0.89[ASN][1000 genomes]
rs34595606	0.91[ASN][1000 genomes]
rs35859525	0.90[ASN][1000 genomes]
rs55750243	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62127189	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62127197	0.88[ASN][1000 genomes]
rs62128635	0.91[ASN][1000 genomes]
rs6711473	0.91[ASN][1000 genomes]
rs6714787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6717431	0.91[ASN][1000 genomes]
rs6720112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.91[ASN][1000 genomes]
rs6721857	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[ASN][1000 genomes]
rs6722126	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[ASN][1000 genomes]
rs6730247	0.91[ASN][1000 genomes]
rs6732429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740245	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6751436	0.91[ASN][1000 genomes]
rs6755281	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs744809	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7572489	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589694	0.88[ASN][1000 genomes]
rs759401	0.87[ASN][1000 genomes]
rs7598541	0.88[ASN][1000 genomes]
rs9287718	0.84[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.88[ASN][1000 genomes]
rs9287721	1.00[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs9973374	0.89[ASN][1000 genomes]
rs9973456	0.89[ASN][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	nsv1007185	chr2:10540386-10791743	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv833370	chr2:10625149-10785402	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1009897	chr2:10627248-10751468	Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1000953	chr2:10717304-10921805	Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv535584	chr2:10717304-10921805	Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv833381	chr2:10723465-10911284	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12476554	CYS1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10698600-10736600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:10705800-10736000	Strong transcription	Duodenum Mucosa	Duodenum
3	chr2:10707400-10728800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:10708600-10732000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr2:10708800-10732800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:10709200-10746800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:10709400-10732600	Strong transcription	Primary B cells from cord blood	blood
8	chr2:10712600-10742000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:10713200-10727800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:10717000-10728800	Weak transcription	Colonic Mucosa	Colon
11	chr2:10717600-10732400	Weak transcription	Fetal Brain Male	brain
12	chr2:10717800-10729000	Weak transcription	Small Intestine	intestine
13	chr2:10718000-10732000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:10719400-10729000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:10719800-10746600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:10720000-10746400	Strong transcription	Dnd41	blood
17	chr2:10720200-10728400	Weak transcription	Psoas Muscle	Psoas
18	chr2:10720400-10728400	Weak transcription	Fetal Lung	lung
19	chr2:10720400-10740200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:10720800-10739200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr2:10721000-10728800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:10721000-10729000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr2:10721000-10755000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr2:10721200-10734600	Strong transcription	GM12878-XiMat	blood
25	chr2:10721200-10746800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:10721400-10727800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr2:10721400-10731200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr2:10721400-10735800	Strong transcription	Primary T cells from cord blood	blood
29	chr2:10721600-10731800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:10721600-10735600	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr2:10721800-10727800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:10721800-10728000	Weak transcription	Brain Angular Gyrus	brain
33	chr2:10722000-10728600	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:10722000-10735200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:10722000-10738200	Strong transcription	Fetal Muscle Leg	muscle
36	chr2:10722400-10734800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr2:10722400-10735200	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr2:10722800-10731400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:10722800-10732400	Strong transcription	Fetal Thymus	thymus
40	chr2:10722800-10741400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:10723000-10728600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr2:10723600-10728600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr2:10723800-10729800	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr2:10724000-10735600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:10724200-10730800	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:10724400-10727800	Weak transcription	Lung	lung
47	chr2:10724400-10728000	Weak transcription	Brain Hippocampus Middle	brain
48	chr2:10724600-10727800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:10724600-10728000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr2:10724600-10728000	Weak transcription	Brain Substantia Nigra	brain

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