Variant report

Variant	rs4930724
Chromosome Location	chr12:124423817-124423818
allele	C/T
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	CTCF	chr12:124423720-124423870	HepG2	liver:	n/a	n/a
2	CTCF	chr12:124423247-124424046	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr12:124423054-124424030	A549	lung:	n/a	chr12:124423095-124423103

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:124423442..124425248-chr12:124427955..124429927,2	MCF-7	breast:
2	chr12:124417812..124421208-chr12:124423467..124426187,5	MCF-7	breast:

Variant related genes	Relation type
DNAH10OS	TF binding region
ENSG00000270005	TF binding region
ENSG00000250091	Chromatin interaction
ENSG00000270005	Chromatin interaction
ENSG00000119242	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1054852	1.00[CHB][hapmap]
rs10773048	0.88[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs10846579	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10846580	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11057393	0.86[EUR][1000 genomes]
rs11057394	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11057396	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs11057397	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs11057399	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057400	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057401	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11057407	1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11057408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs11057409	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs11057412	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11057413	0.91[EUR][1000 genomes]
rs11831913	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11833002	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11835839	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11837287	0.90[CEU][hapmap];0.88[CHB][hapmap];0.91[EUR][1000 genomes]
rs1187415	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12296259	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12298484	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs12301673	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12303671	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12303933	0.91[EUR][1000 genomes]
rs12310367	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs12311114	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12311848	0.90[EUR][1000 genomes]
rs12316080	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12317176	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12809125	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12809473	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs12823740	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12824567	0.83[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs12827409	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs12829951	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12833624	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1882491	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2130382	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs2178663	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3186071	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34114498	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34180676	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34854841	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34878139	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35099862	0.91[EUR][1000 genomes]
rs35825716	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3789967	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3802999	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs4405410	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]
rs4575361	0.81[EUR][1000 genomes]
rs4765127	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4765148	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs4765219	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4765305	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4765335	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4765528	0.83[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs4765541	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4765562	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4765568	1.00[CHB][hapmap]
rs4930721	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs4930722	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4930723	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4930725	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4930726	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55990776	0.85[EUR][1000 genomes]
rs56041971	0.91[EUR][1000 genomes]
rs6488912	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6488913	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6488914	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7131882	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7132655	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7133378	0.94[ASW][hapmap];0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7134121	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7135314	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs71458830	0.90[EUR][1000 genomes]
rs7301953	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs7305864	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7307053	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs7307277	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs7311233	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs7311969	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7312404	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7955815	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7958691	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7961449	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7964945	0.81[JPT][hapmap]
rs7966192	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7973683	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7975482	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs7978610	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs952632	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs9863	0.82[ASW][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9971695	0.94[ASW][hapmap];0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][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	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
2	esv1811815	chr12:124374716-124424636	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv1832870	chr12:124374716-124424636	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv522321	chr12:124383950-124424636	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4930724	RP11-380L11.4	cis	Esophagus Muscularis	GTEx
rs4930724	DNAH10	cis	brain	BrainEAC

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124408800-124428000	Weak transcription	Right Atrium	heart
2	chr12:124409600-124426200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:124417200-124424400	Weak transcription	Colonic Mucosa	Colon
4	chr12:124417600-124443600	Weak transcription	Fetal Kidney	kidney
5	chr12:124417800-124427400	Weak transcription	Fetal Brain Male	brain
6	chr12:124417800-124428400	Strong transcription	Brain Germinal Matrix	brain
7	chr12:124418000-124428400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:124418000-124431000	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr12:124418200-124426200	Strong transcription	Fetal Intestine Small	intestine
10	chr12:124418200-124427800	Strong transcription	Fetal Brain Female	brain
11	chr12:124418200-124430800	Strong transcription	Stomach Smooth Muscle	stomach
12	chr12:124418200-124431400	Strong transcription	Fetal Stomach	stomach
13	chr12:124418600-124430800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:124419000-124428400	Strong transcription	Fetal Muscle Leg	muscle
15	chr12:124419200-124426200	Weak transcription	Fetal Heart	heart
16	chr12:124419400-124426400	Weak transcription	A549	lung
17	chr12:124419800-124425000	Weak transcription	NHDF-Ad	bronchial
18	chr12:124419800-124426000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr12:124419800-124426200	Strong transcription	Fetal Intestine Large	intestine
20	chr12:124420000-124425800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:124420200-124433000	Weak transcription	Small Intestine	intestine
22	chr12:124420600-124426000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:124420600-124430800	Strong transcription	Pancreas	Pancrea
24	chr12:124420800-124425800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:124420800-124427800	Strong transcription	Right Ventricle	heart
26	chr12:124420800-124432600	Weak transcription	HepG2	liver
27	chr12:124421000-124430600	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr12:124421600-124424800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr12:124421600-124426000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:124421600-124427600	Weak transcription	Brain Angular Gyrus	brain
31	chr12:124422000-124424400	Weak transcription	Brain Anterior Caudate	brain
32	chr12:124422000-124426200	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr12:124422200-124424200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr12:124422200-124424200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr12:124422200-124424400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:124422200-124424400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:124422200-124424600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:124422200-124426200	Weak transcription	NHLF	lung
39	chr12:124422200-124426400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr12:124422400-124424400	Weak transcription	Esophagus	oesophagus
41	chr12:124422400-124424400	Weak transcription	Gastric	stomach
42	chr12:124422400-124439200	Weak transcription	Psoas Muscle	Psoas
43	chr12:124422600-124424200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:124422600-124424200	Weak transcription	Brain Substantia Nigra	brain
45	chr12:124422600-124424200	Weak transcription	Left Ventricle	heart
46	chr12:124422600-124424600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr12:124422600-124426000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr12:124422800-124424000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:124423000-124424000	Enhancers	Primary T cells fromperipheralblood	blood
50	chr12:124423000-124426400	Weak transcription	Colon Smooth Muscle	Colon

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