Variant report

Variant	rs4405410
Chromosome Location	chr12:124435788-124435789
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:124409804..124411396-chr12:124435768..124438703,2	K562	blood:
2	chr12:124434208..124435911-chr12:124436038..124437708,2	K562	blood:
3	chr12:124434361..124437617-chr12:124443496..124446942,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197653	Chromatin interaction
ENSG00000270130	Chromatin interaction
ENSG00000270028	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1054852	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs10773048	0.88[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10846579	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10846580	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11057393	0.93[EUR][1000 genomes]
rs11057394	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11057396	1.00[CEU][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11057397	1.00[CEU][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11057399	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057400	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057401	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057407	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11057409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11057412	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11057413	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11831913	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11833002	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11835839	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837287	0.96[CEU][hapmap];0.89[CHB][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1187415	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12296259	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12298484	1.00[CEU][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12301673	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12303671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12303933	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12310367	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12311114	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12311848	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12316080	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12317176	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12809125	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12809473	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12823740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12824567	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12827409	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12829951	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12833624	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1882491	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2130382	0.89[CEU][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2178663	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3186071	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34114498	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34180676	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34854841	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34878139	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35099862	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35825716	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3789967	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802999	1.00[CEU][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4575361	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4765127	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4765148	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4765219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765305	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765335	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765528	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4765541	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4765562	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4765568	1.00[CHB][hapmap]
rs4930721	0.88[CEU][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4930722	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4930723	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4930724	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4930725	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4930726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55990776	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56041971	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6488912	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488913	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488914	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131882	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132655	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133378	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7134121	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7135314	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71458830	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7301953	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs7305864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307053	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7307277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7311233	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7311969	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7312404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7955815	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7958691	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964945	0.90[JPT][hapmap]
rs7966192	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975482	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7978610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs952632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9863	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs9971695	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4405410	RP11-380L11.4	cis	Esophagus Muscularis	GTEx
rs4405410	CCDC92	cis	Heart Left Ventricle	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124417600-124443600	Weak transcription	Fetal Kidney	kidney
2	chr12:124422400-124439200	Weak transcription	Psoas Muscle	Psoas
3	chr12:124423600-124442200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:124426800-124436800	Weak transcription	NHLF	lung
5	chr12:124427000-124455000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:124427200-124436800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:124427200-124456200	Weak transcription	Esophagus	oesophagus
8	chr12:124427400-124436200	Enhancers	Fetal Brain Male	brain
9	chr12:124427800-124436800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:124427800-124444800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:124427800-124453400	Weak transcription	A549	lung
12	chr12:124428400-124455800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:124428400-124456000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:124428800-124436400	Weak transcription	Fetal Heart	heart
15	chr12:124428800-124449800	Weak transcription	HSMM	muscle
16	chr12:124428800-124455800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr12:124430000-124454800	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr12:124430000-124456200	Weak transcription	Fetal Thymus	thymus
19	chr12:124430200-124443600	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:124430200-124445600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:124430200-124453400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:124430200-124455600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:124430400-124443600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:124430400-124449800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr12:124430400-124450400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:124430400-124454800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:124430400-124455800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:124430400-124456000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr12:124430400-124456000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:124430400-124456000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:124430600-124436800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr12:124430600-124441800	Weak transcription	Primary B cells from cord blood	blood
33	chr12:124430600-124443000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:124430600-124452600	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr12:124430600-124456200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:124431000-124443000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:124431200-124436400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:124431800-124437000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:124431800-124455800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr12:124432600-124435800	Enhancers	Fetal Intestine Large	intestine
41	chr12:124432600-124437000	Enhancers	Right Atrium	heart
42	chr12:124433000-124436400	Enhancers	Lung	lung
43	chr12:124433000-124436400	Enhancers	Right Ventricle	heart
44	chr12:124433600-124436800	Weak transcription	Small Intestine	intestine
45	chr12:124433600-124437200	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr12:124433600-124437800	Enhancers	K562	blood
47	chr12:124433800-124436400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr12:124433800-124436600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:124434000-124436400	Weak transcription	NH-A	brain
50	chr12:124434000-124437200	Enhancers	Adipose Nuclei	Adipose

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