Variant report

Variant	rs12128410
Chromosome Location	chr1:212972599-212972600
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	chr1:212963881..212969695-chr1:212970420..212976060,10	K562	blood:
2	chr1:212967889..212970692-chr1:212972432..212975770,4	K562	blood:

Variant related genes	Relation type
ENSG00000117697	Chromatin interaction
ENSG00000203705	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10127512	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10127703	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10127756	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1046083	0.97[EUR][1000 genomes]
rs10863989	0.94[EUR][1000 genomes]
rs10863997	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11120001	0.88[EUR][1000 genomes]
rs11120007	0.84[CEU][hapmap];0.97[EUR][1000 genomes]
rs11120014	0.90[GIH][hapmap]
rs11120017	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11120029	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120030	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120035	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11120036	0.91[ASN][1000 genomes]
rs11120042	0.86[YRI][hapmap]
rs11556187	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11800642	0.97[EUR][1000 genomes]
rs11805669	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11806535	0.97[EUR][1000 genomes]
rs11808846	0.90[GIH][hapmap]
rs11809232	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11809382	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11810895	0.94[EUR][1000 genomes]
rs11811017	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12036054	0.91[ASN][1000 genomes]
rs12128903	0.95[EUR][1000 genomes]
rs12129933	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12130072	0.94[ASN][1000 genomes]
rs12133124	0.91[ASN][1000 genomes]
rs12136656	0.91[ASN][1000 genomes]
rs12137768	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12140831	0.85[YRI][hapmap]
rs12409787	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12729663	0.94[EUR][1000 genomes]
rs13376317	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13376383	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13376390	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1507357	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs1507358	0.90[GIH][hapmap]
rs1532951	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17019726	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271148	0.93[GIH][hapmap]
rs2358899	0.97[EUR][1000 genomes]
rs34110137	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35213366	0.90[EUR][1000 genomes]
rs3738798	0.90[GIH][hapmap]
rs3738803	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55840547	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56088044	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56243109	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59231663	0.95[EUR][1000 genomes]
rs60308869	0.97[EUR][1000 genomes]
rs6540760	0.97[EUR][1000 genomes]
rs6540762	0.90[GIH][hapmap]
rs6662981	0.94[EUR][1000 genomes]
rs6670648	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6671866	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6681171	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs6687672	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6688238	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6694190	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[LWK][hapmap];0.91[ASN][1000 genomes]
rs6694448	0.97[EUR][1000 genomes]
rs6700204	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6702101	0.90[GIH][hapmap]
rs73081853	0.97[EUR][1000 genomes]
rs73081902	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73083707	0.96[EUR][1000 genomes]
rs73083727	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73083731	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73083749	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73083756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73083765	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73083778	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7515115	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7516312	1.00[CEU][hapmap];0.96[GIH][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7519582	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524203	0.86[YRI][hapmap]
rs7525518	0.94[EUR][1000 genomes]
rs7527216	0.95[EUR][1000 genomes]
rs7536629	0.94[EUR][1000 genomes]
rs7538755	0.97[EUR][1000 genomes]
rs7544645	0.81[YRI][hapmap]
rs7546462	0.94[EUR][1000 genomes]
rs7546564	0.94[EUR][1000 genomes]
rs7546754	0.96[EUR][1000 genomes]
rs7548861	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552880	0.99[EUR][1000 genomes]
rs7552899	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv2756884	chr1:212925429-213006397	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2758997	chr1:212925429-213006397	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1010003	chr1:212944240-212986996	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12128410	SNORA16B	cis	cerebellum	SCAN
rs12128410	LOC642946	cis	multi-tissue	Pritchard
rs12128410	NSL1	cis	parietal	SCAN
rs12128410	TATDN3	cis	Artery Tibial	GTEx
rs12128410	TATDN3	cis	multi-tissue	Pritchard
rs12128410	SNFT	cis	multi-tissue	Pritchard
rs12128410	BATF3	cis	cerebellum	SCAN
rs12128410	FLVCR1	cis	lymphoblastoid	seeQTL
rs12128410	NCRNA00292	cis	lymphoblastoid	seeQTL
rs12128410	SLC30A1	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212965800-212992600	Weak transcription	Lung	lung
2	chr1:212966000-212974800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:212966000-212981200	Weak transcription	Esophagus	oesophagus
4	chr1:212966000-212983000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:212966000-212997400	Weak transcription	Aorta	Aorta
6	chr1:212966200-212973800	Weak transcription	Colonic Mucosa	Colon
7	chr1:212966200-212975600	Weak transcription	HMEC	breast
8	chr1:212966200-212979800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:212966400-212977400	Weak transcription	Hela-S3	cervix
10	chr1:212966400-212984000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:212966400-212985600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:212966400-212988200	Weak transcription	Fetal Heart	heart
13	chr1:212966400-212989600	Weak transcription	Fetal Brain Male	brain
14	chr1:212966400-212990200	Weak transcription	Right Ventricle	heart
15	chr1:212966800-212977600	Weak transcription	Brain Germinal Matrix	brain
16	chr1:212966800-212989600	Weak transcription	Psoas Muscle	Psoas
17	chr1:212967000-212979000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:212967000-212984400	Weak transcription	Spleen	Spleen
19	chr1:212967200-212975400	Weak transcription	HSMM	muscle
20	chr1:212967200-212984000	Weak transcription	NHDF-Ad	bronchial
21	chr1:212967200-212988400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:212967200-212989000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:212967200-212989600	Weak transcription	NHLF	lung
24	chr1:212968000-212980000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:212968000-212987400	Weak transcription	Fetal Intestine Large	intestine
26	chr1:212968400-212974400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr1:212968400-212988000	Weak transcription	Stomach Mucosa	stomach
28	chr1:212968600-212980200	Weak transcription	HUVEC	blood vessel
29	chr1:212968800-212974600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:212969000-212972600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:212969000-212973400	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr1:212969000-212973800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:212969000-212975400	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:212969000-212976200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:212969000-212976400	Strong transcription	Liver	Liver
36	chr1:212969000-212980000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:212969000-212980000	Strong transcription	Dnd41	blood
38	chr1:212969000-212982600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:212969000-212982600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:212969000-212983000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:212969200-212973400	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr1:212969200-212976200	Strong transcription	Fetal Thymus	thymus
43	chr1:212969400-212972800	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:212969400-212978600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:212969600-212989000	Weak transcription	HepG2	liver
46	chr1:212969600-212993000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:212969800-212975000	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:212970000-212972600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:212970000-212972600	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr1:212970000-212972600	Strong transcription	Brain Anterior Caudate	brain

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