Variant report

Variant	rs12775743
Chromosome Location	chr10:43724215-43724216
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43699342..43701842-chr10:43722370..43724384,2	K562	blood:
2	chr10:43717975..43720515-chr10:43721363..43724311,2	MCF-7	breast:
3	chr10:43715924..43718494-chr10:43721120..43724521,4	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10159558	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11238441	0.86[AMR][1000 genomes]
rs11238465	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12258585	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12260994	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12262152	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12765436	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12765715	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12765838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12766298	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12775330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12779732	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12783340	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs17158594	0.81[CHD][hapmap]
rs17158616	0.82[ASW][hapmap];0.81[LWK][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes]
rs17158630	0.88[AFR][1000 genomes]
rs17363630	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1799939	0.90[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs1800863	0.86[AMR][1000 genomes]
rs1864393	0.84[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1879298	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1879299	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2075911	0.86[AMR][1000 genomes]
rs2435351	0.82[CHD][hapmap]
rs2472741	0.82[CHD][hapmap]
rs28401552	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2900627	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3026776	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3026779	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3026781	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3026782	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34817887	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4987091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66557659	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7067798	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs7074319	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7086299	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7092548	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7096367	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs71505665	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs71505667	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71505668	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72783237	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72783242	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72783250	0.84[AFR][1000 genomes]
rs7893332	0.84[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7903283	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7910648	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7910805	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7921281	0.82[ASW][hapmap];0.91[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7923256	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9804209	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv895082	chr10:43530071-43755506	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv895083	chr10:43549708-43765485	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic 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 miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv916378	chr10:43622151-43868356	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv1831010	chr10:43674916-43759185	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv895084	chr10:43688505-43765485	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv466881	chr10:43695049-43799588	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv550696	chr10:43695049-43799588	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv895085	chr10:43695049-43804617	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv825351	chr10:43714249-43788481	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv1035873	chr10:43721143-43873664	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv466882	chr10:43721481-43849358	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
16	nsv550697	chr10:43721481-43849358	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12775743	ZNF22	cis	parietal	SCAN
rs12775743	RET	cis	parietal	SCAN
rs12775743	TXNDC3	trans	lymphoblastoid	seeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43699400-43724600	Weak transcription	Right Atrium	heart
2	chr10:43720600-43724400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr10:43720800-43724600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr10:43721000-43724600	Enhancers	Spleen	Spleen
5	chr10:43723600-43724400	Bivalent Enhancer	Fetal Thymus	thymus
6	chr10:43723800-43724400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
7	chr10:43723800-43724400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr10:43723800-43724600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
9	chr10:43724000-43724400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
10	chr10:43724000-43724400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
11	chr10:43724000-43724400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
12	chr10:43724000-43724400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr10:43724000-43724400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
14	chr10:43724000-43724400	Enhancers	Esophagus	oesophagus
15	chr10:43724000-43724400	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
16	chr10:43724000-43724400	Bivalent Enhancer	Thymus	Thymus
17	chr10:43724000-43724600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr10:43724000-43724600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
19	chr10:43724000-43724600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr10:43724000-43724600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr10:43724000-43724600	Bivalent Enhancer	Gastric	stomach
22	chr10:43724000-43724800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
23	chr10:43724000-43724800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
24	chr10:43724000-43725800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
25	chr10:43724000-43726000	Bivalent Enhancer	Fetal Muscle Leg	muscle
26	chr10:43724200-43724400	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr10:43724200-43724400	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
28	chr10:43724200-43724400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
29	chr10:43724200-43724400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
30	chr10:43724200-43724400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
31	chr10:43724200-43724400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
32	chr10:43724200-43724400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr10:43724200-43724400	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
34	chr10:43724200-43724400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr10:43724200-43724400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr10:43724200-43724400	Bivalent Enhancer	Liver	Liver
37	chr10:43724200-43724400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
38	chr10:43724200-43724400	Bivalent Enhancer	Small Intestine	intestine
39	chr10:43724200-43724400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
40	chr10:43724200-43724600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr10:43724200-43724600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
42	chr10:43724200-43724600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr10:43724200-43724600	Bivalent Enhancer	Primary B cells from cord blood	blood
44	chr10:43724200-43724600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
45	chr10:43724200-43724600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr10:43724200-43724600	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
47	chr10:43724200-43724600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr10:43724200-43724600	Active TSS	Brain Angular Gyrus	brain
49	chr10:43724200-43724600	Enhancers	Pancreas	Pancrea
50	chr10:43724200-43724600	Bivalent Enhancer	Right Ventricle	heart

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