Variant report

Variant	rs12232410
Chromosome Location	chr16:69736851-69736852
allele	A/G
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	chr16:69736755-69736855	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr16:69735702-69739032	A549	lung:	n/a	n/a
3	BCL3	chr16:69736686-69739074	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:69709143..69710860-chr16:69736738..69738963,2	K562	blood:
2	chr16:69734561..69737941-chr16:69738671..69742586,5	MCF-7	breast:
3	chr16:69736062..69737792-chr16:69760571..69762249,2	K562	blood:

Variant related genes	Relation type
ENSG00000260772	TF binding region
ENSG00000238683	Chromatin interaction
ENSG00000262136	Chromatin interaction
ENSG00000181019	Chromatin interaction
ENSG00000102908	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10048108	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10163235	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10454066	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10500551	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10852457	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10852458	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11075727	0.82[EUR][1000 genomes]
rs11075728	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11075730	0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[ASN][1000 genomes]
rs11075733	0.84[EUR][1000 genomes]
rs11075734	0.95[CEU][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs1139178	0.85[EUR][1000 genomes]
rs11639947	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11641050	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11641233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11642030	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11642115	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11643240	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11643530	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11643926	0.82[EUR][1000 genomes]
rs11646884	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12447326	0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12447883	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12449005	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12595869	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12595878	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12595927	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12596679	0.95[CEU][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap]
rs12596823	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12925371	0.85[EUR][1000 genomes]
rs13337236	0.92[ASN][1000 genomes]
rs1437135	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1437136	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16958970	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16959025	0.95[CEU][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs16959035	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1800566	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1865965	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118220	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2161631	0.94[CEU][hapmap];0.81[JPT][hapmap]
rs2196574	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2217950	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2361838	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2361839	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3169315	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3743673	0.94[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3885612	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4464069	0.95[CEU][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap]
rs4497676	0.95[CEU][hapmap]
rs4985518	0.95[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs4985523	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs55701476	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55751101	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55863174	0.80[EUR][1000 genomes]
rs56316408	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57488237	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57565297	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60010276	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60472033	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61310815	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61426398	0.85[EUR][1000 genomes]
rs61460899	0.90[ASN][1000 genomes]
rs6499239	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6499253	0.82[EUR][1000 genomes]
rs6499255	0.95[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs689455	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7186002	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7187653	0.94[CEU][hapmap]
rs7189424	0.85[EUR][1000 genomes]
rs7190652	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7194753	0.95[CEU][hapmap];0.82[CHD][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap]
rs7196943	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7198242	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7200935	0.95[CEU][hapmap];0.84[CHD][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap]
rs72783115	0.94[ASN][1000 genomes]
rs73579458	0.82[EUR][1000 genomes]
rs74026882	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74029403	0.95[EUR][1000 genomes]
rs8045142	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8045682	0.95[CEU][hapmap];0.95[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs8046314	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8047885	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8052086	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8053080	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8054000	0.88[ASN][1000 genomes]
rs8054096	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8059345	0.82[EUR][1000 genomes]
rs8060588	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs920191	0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.92[ASN][1000 genomes]
rs9788803	0.92[ASN][1000 genomes]
rs9788837	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9921045	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9929720	0.95[CEU][hapmap];0.84[CHD][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap]
rs9933526	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9940548	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906822	chr16:69711533-69745145	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	esv3396845	chr16:69721905-69770627	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12232410	SLC7A6	cis	cerebellum	SCAN
rs12232410	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs12232410	TPPP3	cis	parietal	SCAN
rs12232410	NRN1L	cis	cerebellum	SCAN
rs12232410	HPR	cis	cerebellum	SCAN
rs12232410	FAM96B	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69701800-69739200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr16:69704600-69737800	Strong transcription	Liver	Liver
3	chr16:69708800-69739600	Strong transcription	Placenta	Placenta
4	chr16:69709000-69739400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr16:69709400-69755400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr16:69709800-69737000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr16:69710000-69737400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr16:69715200-69737800	Strong transcription	HepG2	liver
9	chr16:69722400-69737200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr16:69722600-69738800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr16:69722800-69739400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr16:69723800-69739200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr16:69724600-69738400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr16:69726000-69755800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr16:69726600-69738800	Strong transcription	HSMM	muscle
16	chr16:69726600-69759800	Weak transcription	Psoas Muscle	Psoas
17	chr16:69726800-69737200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr16:69726800-69739000	Strong transcription	GM12878-XiMat	blood
19	chr16:69726800-69747600	Weak transcription	Fetal Heart	heart
20	chr16:69727600-69737800	Weak transcription	Right Atrium	heart
21	chr16:69728200-69746200	Weak transcription	Stomach Mucosa	stomach
22	chr16:69728200-69758600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr16:69728400-69740200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr16:69728400-69744200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr16:69728400-69748800	Weak transcription	Gastric	stomach
26	chr16:69728400-69759200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr16:69728600-69752000	Weak transcription	Fetal Brain Male	brain
28	chr16:69729200-69737000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr16:69729200-69739800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr16:69729200-69745000	Weak transcription	Spleen	Spleen
31	chr16:69729400-69741400	Weak transcription	Lung	lung
32	chr16:69729400-69741600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr16:69729400-69743600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr16:69729400-69744800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr16:69729400-69745000	Weak transcription	Pancreas	Pancrea
36	chr16:69729400-69760000	Weak transcription	Brain Germinal Matrix	brain
37	chr16:69729400-69760000	Weak transcription	Ovary	ovary
38	chr16:69729600-69739200	Weak transcription	Fetal Intestine Small	intestine
39	chr16:69729600-69739200	Weak transcription	Fetal Stomach	stomach
40	chr16:69729600-69740800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr16:69729600-69745000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr16:69729800-69746200	Weak transcription	Aorta	Aorta
43	chr16:69729800-69746200	Weak transcription	Left Ventricle	heart
44	chr16:69729800-69748800	Weak transcription	Esophagus	oesophagus
45	chr16:69730000-69739400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr16:69730000-69740600	Weak transcription	Small Intestine	intestine
47	chr16:69730000-69743400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr16:69730000-69743400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr16:69730000-69743600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr16:69730000-69745200	Weak transcription	Thymus	Thymus

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