Variant report

Variant	rs12229607
Chromosome Location	chr12:118776138-118776139
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:118773930..118776516-chr12:118779431..118781891,3	K562	blood:
2	chr12:118769840..118772299-chr12:118773949..118776713,2	K562	blood:
3	chr12:118775460..118777770-chr12:118780003..118783654,3	K562	blood:
4	chr12:118774312..118778410-chr12:118809648..118812658,5	K562	blood:

Variant related genes	Relation type
ENSG00000135090	Chromatin interaction

Extended variants
information (count: 177 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:172)

rs_ID	r²[population]
rs10507286	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1060964	0.92[CEU][hapmap]
rs10850967	0.93[CEU][hapmap]
rs11068853	0.80[CHB][hapmap]
rs11068856	0.80[CHB][hapmap]
rs11068870	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11068878	0.86[ASN][1000 genomes]
rs11068880	0.87[CHB][hapmap];0.88[ASN][1000 genomes]
rs11068881	0.88[ASN][1000 genomes]
rs11068887	0.86[ASN][1000 genomes]
rs11068888	0.87[ASN][1000 genomes]
rs11068889	0.87[ASN][1000 genomes]
rs11068891	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11068892	0.89[ASN][1000 genomes]
rs11068893	0.87[CHB][hapmap];0.89[ASN][1000 genomes]
rs11068896	0.86[ASN][1000 genomes]
rs11068898	0.86[CHB][hapmap];0.91[ASN][1000 genomes]
rs11068899	0.91[ASN][1000 genomes]
rs11068900	0.87[CHB][hapmap]
rs11068901	0.86[CHB][hapmap];0.91[ASN][1000 genomes]
rs11068904	0.81[CHB][hapmap];0.91[ASN][1000 genomes]
rs11068906	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11068908	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11068909	0.86[CHB][hapmap];0.91[ASN][1000 genomes]
rs11068910	0.95[EUR][1000 genomes]
rs11068914	0.92[ASN][1000 genomes]
rs11068915	0.87[CHB][hapmap];0.92[ASN][1000 genomes]
rs11068916	0.87[CHB][hapmap];0.89[ASN][1000 genomes]
rs11068917	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11068919	0.93[CEU][hapmap];0.88[CHB][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11068920	0.89[ASN][1000 genomes]
rs11068922	0.88[ASN][1000 genomes]
rs11068923	0.87[ASN][1000 genomes]
rs11068924	0.88[ASN][1000 genomes]
rs11068926	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11068930	0.83[ASN][1000 genomes]
rs12227411	0.91[ASN][1000 genomes]
rs12227974	0.86[CHB][hapmap];0.91[ASN][1000 genomes]
rs12228425	0.86[CHB][hapmap];0.91[ASN][1000 genomes]
rs12230104	0.83[ASN][1000 genomes]
rs12231358	0.89[ASN][1000 genomes]
rs12231845	0.89[ASN][1000 genomes]
rs12308475	0.94[EUR][1000 genomes]
rs16948193	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs16948197	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs16948204	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs16948230	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs16948234	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs16948250	0.93[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs17433217	0.86[EUR][1000 genomes]
rs17440315	0.92[CEU][hapmap]
rs17440336	0.92[CEU][hapmap]
rs17440364	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs17440433	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs17440669	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs17440774	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs17440823	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17440893	0.93[CEU][hapmap]
rs17440942	0.93[CEU][hapmap]
rs17440956	0.93[CEU][hapmap]
rs17441033	0.84[CEU][hapmap]
rs17441061	0.93[CEU][hapmap]
rs17441075	0.85[CEU][hapmap]
rs17512142	0.92[CEU][hapmap]
rs17512177	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs17512198	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs17512219	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs17512407	1.00[CEU][hapmap]
rs17512483	0.93[CEU][hapmap]
rs17512525	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs17512574	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17512609	1.00[CEU][hapmap]
rs17512644	0.93[CEU][hapmap]
rs17512652	0.93[CEU][hapmap]
rs17512763	0.93[CEU][hapmap]
rs17586342	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[YRI][hapmap]
rs17586582	0.87[CHB][hapmap];0.88[ASN][1000 genomes]
rs17619702	0.83[CHB][hapmap];0.88[ASN][1000 genomes]
rs17619805	0.87[CHB][hapmap];0.91[ASN][1000 genomes]
rs17619932	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2036314	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2055534	0.93[CEU][hapmap]
rs2062519	0.93[CEU][hapmap]
rs2062520	0.88[ASN][1000 genomes]
rs2271007	0.80[ASN][1000 genomes]
rs2280711	0.92[CEU][hapmap];0.86[CHB][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2784	0.93[CEU][hapmap]
rs3852532	0.86[EUR][1000 genomes]
rs4442583	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4766899	0.93[CEU][hapmap]
rs4766900	0.93[CEU][hapmap]
rs4767669	0.93[CEU][hapmap]
rs4767670	0.93[CEU][hapmap]
rs4767671	0.93[CEU][hapmap]
rs4767672	0.93[CEU][hapmap]
rs55833534	0.88[EUR][1000 genomes]
rs56033674	0.86[EUR][1000 genomes]
rs56284927	0.81[EUR][1000 genomes]
rs56708462	0.88[EUR][1000 genomes]
rs58113338	0.86[EUR][1000 genomes]
rs61943364	0.91[EUR][1000 genomes]
rs61943365	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61943369	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61943370	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61943371	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61945175	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61945176	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61945177	0.81[EUR][1000 genomes]
rs61945180	0.83[EUR][1000 genomes]
rs61945181	0.83[EUR][1000 genomes]
rs61945182	0.86[EUR][1000 genomes]
rs61945183	0.86[EUR][1000 genomes]
rs61945184	0.86[EUR][1000 genomes]
rs61945187	0.86[EUR][1000 genomes]
rs61945188	0.86[EUR][1000 genomes]
rs61945190	0.84[EUR][1000 genomes]
rs61945192	0.86[EUR][1000 genomes]
rs61945206	0.86[EUR][1000 genomes]
rs61945207	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61945210	0.85[EUR][1000 genomes]
rs61945212	0.86[EUR][1000 genomes]
rs61945216	0.86[EUR][1000 genomes]
rs61945218	0.85[EUR][1000 genomes]
rs61945219	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61945220	0.86[EUR][1000 genomes]
rs61945221	0.86[EUR][1000 genomes]
rs61945226	0.86[EUR][1000 genomes]
rs61945228	0.88[EUR][1000 genomes]
rs61946063	0.94[EUR][1000 genomes]
rs61946067	0.87[EUR][1000 genomes]
rs61946068	0.89[EUR][1000 genomes]
rs6490173	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6490175	0.91[EUR][1000 genomes]
rs6490177	0.92[CEU][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7132582	0.89[ASN][1000 genomes]
rs7136216	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[YRI][hapmap];0.85[EUR][1000 genomes]
rs7136676	0.93[CEU][hapmap]
rs7137055	0.93[CEU][hapmap]
rs7294498	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs7295288	0.93[CEU][hapmap]
rs7296216	0.88[ASN][1000 genomes]
rs7299040	0.93[CEU][hapmap]
rs7302387	1.00[CEU][hapmap]
rs7303417	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7304342	0.93[CEU][hapmap]
rs7305647	0.93[CEU][hapmap]
rs7307393	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs7309484	0.93[CEU][hapmap]
rs7309671	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs7312555	0.93[CEU][hapmap]
rs7314987	1.00[CEU][hapmap]
rs73205512	0.86[EUR][1000 genomes]
rs73205526	0.86[EUR][1000 genomes]
rs73205531	0.88[EUR][1000 genomes]
rs73205551	0.94[EUR][1000 genomes]
rs73222058	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7954330	0.85[EUR][1000 genomes]
rs7957828	0.94[EUR][1000 genomes]
rs7961312	1.00[CEU][hapmap]
rs7962185	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7963353	0.86[EUR][1000 genomes]
rs7963464	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7965350	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7967900	0.85[CEU][hapmap]
rs7970481	0.86[EUR][1000 genomes]
rs7974718	0.87[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7977403	0.84[EUR][1000 genomes]
rs884844	0.93[CEU][hapmap]
rs965524	0.93[CEU][hapmap]
rs9669004	0.86[EUR][1000 genomes]
rs9888447	0.85[CHB][hapmap];0.91[ASN][1000 genomes]
rs9943819	1.00[CEU][hapmap];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats 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
2	nsv1038224	chr12:118648415-118791388	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1040061	chr12:118648415-118800437	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1053417	chr12:118688969-118808530	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv560390	chr12:118756336-118778232	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118720800-118793600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:118746000-118783200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr12:118746200-118785000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:118752800-118783200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr12:118754600-118782200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:118767400-118778600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:118768400-118776600	Weak transcription	Fetal Stomach	stomach
8	chr12:118768800-118790400	Weak transcription	Primary T cells from cord blood	blood
9	chr12:118769000-118778000	Weak transcription	Stomach Mucosa	stomach
10	chr12:118769000-118783200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr12:118769000-118783200	Weak transcription	Brain Anterior Caudate	brain
12	chr12:118769000-118784000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr12:118769200-118776200	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr12:118769200-118776600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr12:118769200-118782000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr12:118769200-118783200	Weak transcription	Gastric	stomach
17	chr12:118769200-118785000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:118769200-118785800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr12:118769200-118791000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:118769800-118782600	Weak transcription	Fetal Intestine Small	intestine
21	chr12:118770000-118785200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr12:118770600-118776200	Weak transcription	K562	blood
23	chr12:118770600-118780400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr12:118771800-118776600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr12:118773000-118776200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:118773200-118776400	Enhancers	Hela-S3	cervix
27	chr12:118773600-118780400	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr12:118773800-118777000	Enhancers	NHDF-Ad	bronchial
29	chr12:118774000-118776200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:118774000-118792400	Weak transcription	Dnd41	blood
31	chr12:118774200-118776200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:118774200-118776800	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr12:118774200-118782000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr12:118774600-118776400	Enhancers	Fetal Lung	lung
35	chr12:118774800-118783200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:118775000-118777000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:118775200-118776200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:118775400-118777000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:118775600-118776400	Enhancers	NHLF	lung
40	chr12:118775600-118776600	Enhancers	GM12878-XiMat	blood
41	chr12:118775800-118777000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr12:118775800-118777000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr12:118775800-118778200	Enhancers	A549	lung
44	chr12:118775800-118783000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:118775800-118792000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:118775800-118792600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr12:118776000-118782000	Weak transcription	Primary B cells from cord blood	blood

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