Variant report

Variant	rs12122399
Chromosome Location	chr1:174964850-174964851
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:174964682-174965635	GM12892	blood:	n/a	n/a
2	POLR2A	chr1:174964460-174965643	H1-hESC	embryonic stem cell:	n/a	n/a
3	ATF2	chr1:174964550-174965123	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr1:174962895-174965327	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:174964471-174964999	H1-hESC	embryonic stem cell:	n/a	n/a
6	JUN	chr1:174964778-174966321	K562	blood:	n/a	n/a
7	POLR2A	chr1:174963970-174972111	K562	blood:	n/a	n/a
8	NFATC1	chr1:174964816-174966938	GM12878	blood:	n/a	n/a
9	FOXA1	chr1:174964108-174964997	HepG2	liver:	n/a	n/a
10	POLR2A	chr1:174964509-174966297	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr1:174964510-174965013	GM12892	blood:	n/a	n/a
12	POLR2A	chr1:174964685-174964931	H1-hESC	embryonic stem cell:	n/a	n/a
13	FOXA2	chr1:174964027-174964914	HepG2	liver:	n/a	n/a
14	POLR2A	chr1:174964730-174964903	GM12891	blood:	n/a	n/a
15	SP4	chr1:174964722-174965048	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr1:174961977-174964877	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:174943613..174945590-chr1:174962793..174965614,2	MCF-7	breast:
2	chr1:174932418..174935374-chr1:174964535..174970014,5	K562	blood:
3	chr1:174768282..174770482-chr1:174964486..174966155,2	MCF-7	breast:
4	chr1:174963484..174965002-chr8:144948053..144950933,2	MCF-7	breast:
5	chr1:174927580..174945830-chr1:174955726..174971213,32	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MRPS14-1	chr1:174964447-174968075	NONHSAT007742

No data

Variant related genes	Relation type
RNU6-307P	TF binding region
CACYBP	TF binding region
ENSG00000152061	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10912860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10912867	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11582831	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12119351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122361	1.00[CHB][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap]
rs12124150	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12125682	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12723394	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12753457	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34484492	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56978149	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59663317	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691857	1.00[CHB][hapmap]
rs6700816	1.00[CHB][hapmap]
rs7537508	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550448	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1001000	chr1:174944208-174978853	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12122399	RC3H1	Cis_chr	lymphoblastoid	RTeQTL
rs12122399	PRDX6	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174924200-174967800	Weak transcription	Brain Germinal Matrix	brain
2	chr1:174935000-174967000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:174938600-174965200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:174940000-174967600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:174941000-174968000	Weak transcription	Gastric	stomach
6	chr1:174944400-174967800	Weak transcription	Aorta	Aorta
7	chr1:174944800-174967800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:174944800-174968000	Weak transcription	Spleen	Spleen
9	chr1:174946000-174968000	Weak transcription	Lung	lung
10	chr1:174949000-174967800	Weak transcription	Fetal Stomach	stomach
11	chr1:174952200-174967800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:174952400-174968000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:174952800-174965800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:174954800-174968000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:174956000-174967800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:174956200-174967400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:174959000-174965000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:174959600-174967400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:174960000-174965800	Weak transcription	HSMM	muscle
20	chr1:174960000-174967200	Weak transcription	Fetal Thymus	thymus
21	chr1:174960000-174967200	Weak transcription	Left Ventricle	heart
22	chr1:174960000-174967800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:174960000-174968000	Weak transcription	Esophagus	oesophagus
24	chr1:174960200-174965000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:174960200-174965000	Weak transcription	K562	blood
26	chr1:174960200-174965200	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr1:174960200-174965800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr1:174960200-174966400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:174960200-174967000	Weak transcription	Primary T cells from cord blood	blood
30	chr1:174960200-174967000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr1:174960200-174967000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr1:174960200-174967200	Weak transcription	Primary B cells from peripheral blood	blood
33	chr1:174960200-174967200	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr1:174960200-174967200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:174960200-174967200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:174960200-174967200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:174960200-174967400	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:174960200-174967400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:174960200-174967400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:174960200-174967400	Weak transcription	A549	lung
41	chr1:174960200-174967600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr1:174960200-174967600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr1:174960200-174967600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr1:174960200-174967600	Weak transcription	Thymus	Thymus
45	chr1:174960200-174967800	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr1:174960200-174967800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:174960200-174967800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:174960200-174967800	Weak transcription	Fetal Muscle Leg	muscle
49	chr1:174960200-174967800	Weak transcription	HSMMtube	muscle
50	chr1:174960400-174965600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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