Variant report

Variant	rs7301377
Chromosome Location	chr12:124076254-124076255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:124075113..124078209-chr12:124084747..124087689,4	K562	blood:
2	chr12:124075051..124078239-chr12:124079848..124084285,5	K562	blood:

Variant related genes	Relation type
ENSG00000111364	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11057298	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11057302	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057306	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11610013	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615043	0.81[EUR][1000 genomes]
rs11829661	0.84[AFR][1000 genomes]
rs11834369	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837236	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12099981	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12099985	0.90[AFR][1000 genomes]
rs12099986	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877365	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2340691	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3209852	0.81[ASN][1000 genomes]
rs34099549	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850953	0.88[AFR][1000 genomes]
rs4930715	0.96[EUR][1000 genomes]
rs61678733	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488881	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6488882	0.84[AFR][1000 genomes]
rs7136101	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7303554	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316613	0.94[EUR][1000 genomes]
rs73414262	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs786428	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786429	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786431	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786432	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786433	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786434	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786435	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786437	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786438	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786439	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786450	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786455	0.80[EUR][1000 genomes]
rs7954782	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7958153	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960812	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964934	0.85[AFR][1000 genomes]
rs7965292	0.90[AFR][1000 genomes]
rs7965466	0.84[EUR][1000 genomes]
rs7968040	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970545	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971779	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973187	0.88[AFR][1000 genomes]
rs7973689	0.88[AFR][1000 genomes]
rs952360	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	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
6	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7301377	RP11-486O12.2	cis	Adipose Subcutaneous	GTEx
rs7301377	DDX55	cis	Esophagus Muscularis	GTEx
rs7301377	DDX55	cis	Thyroid	GTEx
rs7301377	RP11-486O12.2	cis	Heart Left Ventricle	GTEx
rs7301377	RP11-486O12.2	cis	Esophagus Mucosa	GTEx
rs7301377	RP11-486O12.2	cis	Muscle Skeletal	GTEx
rs7301377	RP11-486O12.2	cis	Thyroid	GTEx
rs7301377	DDX55	cis	lung	GTEx
rs7301377	RP11-486O12.2	cis	Artery Aorta	GTEx
rs7301377	RP11-486O12.2	cis	Nerve Tibial	GTEx
rs7301377	RP11-486O12.2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124070000-124085800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:124070400-124076400	Weak transcription	Ovary	ovary
3	chr12:124070400-124076600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:124070600-124082200	Strong transcription	Fetal Muscle Leg	muscle
5	chr12:124070600-124084400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:124070800-124077200	Genic enhancers	HUVEC	blood vessel
7	chr12:124071000-124077400	Genic enhancers	HepG2	liver
8	chr12:124071200-124077200	Strong transcription	Fetal Lung	lung
9	chr12:124071200-124077400	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:124071200-124082800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:124071200-124083400	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr12:124071200-124083400	Strong transcription	Fetal Intestine Large	intestine
13	chr12:124071200-124083600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr12:124071200-124083600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr12:124071200-124083600	Strong transcription	Fetal Muscle Trunk	muscle
16	chr12:124071200-124083800	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:124071200-124083800	Strong transcription	Placenta	Placenta
18	chr12:124071200-124084000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:124071200-124084000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr12:124071200-124084800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr12:124071400-124077600	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr12:124071400-124082800	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr12:124071400-124083000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:124071600-124084400	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr12:124071800-124083600	Strong transcription	Primary hematopoietic stem cells	blood
26	chr12:124072200-124085800	Weak transcription	Small Intestine	intestine
27	chr12:124072400-124076800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:124072400-124077000	Strong transcription	Primary B cells from cord blood	blood
29	chr12:124072400-124077000	Strong transcription	HSMMtube	muscle
30	chr12:124072400-124082200	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr12:124072400-124083800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:124072600-124079200	Strong transcription	Placenta Amnion	Placenta Amnion
33	chr12:124072600-124082400	Strong transcription	Thymus	Thymus
34	chr12:124072600-124083400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:124072600-124083400	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr12:124072800-124077400	Strong transcription	Brain Anterior Caudate	brain
37	chr12:124072800-124077400	Strong transcription	HSMM	muscle
38	chr12:124072800-124084200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:124073000-124083600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr12:124073200-124079400	Strong transcription	Fetal Intestine Small	intestine
41	chr12:124073200-124084200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:124073400-124076400	Strong transcription	A549	lung
43	chr12:124073400-124077400	Strong transcription	Brain Hippocampus Middle	brain
44	chr12:124073400-124082400	Strong transcription	NHEK	skin
45	chr12:124073400-124084000	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr12:124073600-124077400	Strong transcription	HMEC	breast
47	chr12:124073600-124077600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:124073600-124080400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr12:124073600-124081600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr12:124073600-124081800	Strong transcription	Colonic Mucosa	Colon

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