Variant report

Variant	rs12993210
Chromosome Location	chr2:11506538-11506539
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	CEBPB	chr2:11506526-11506660	H1-hESC	embryonic stem cell:	n/a	chr2:11506637-11506648
2	FOXA2	chr2:11506340-11506805	HepG2	liver:	n/a	n/a
3	MYBL2	chr2:11506242-11506914	HepG2	liver:	n/a	n/a
4	JUND	chr2:11506463-11506764	HepG2	liver:	n/a	n/a
5	TCF7L2	chr2:11506530-11506761	Hela-S3	cervix:	n/a	n/a
6	FOXA1	chr2:11506220-11506896	HepG2	liver:	n/a	n/a
7	NR2F2	chr2:11506309-11506990	HepG2	liver:	n/a	n/a
8	TCF12	chr2:11506362-11506832	HepG2	liver:	n/a	n/a
9	ELF1	chr2:11506527-11506815	HepG2	liver:	n/a	n/a
10	HNF4G	chr2:11506366-11506778	HepG2	liver:	n/a	n/a
11	REST	chr2:11506378-11506841	HepG2	liver:	n/a	n/a
12	CEBPB	chr2:11506422-11506803	HepG2	liver:	n/a	chr2:11506637-11506648
13	ARID3A	chr2:11505103-11506863	HepG2	liver:	n/a	n/a
14	RAD21	chr2:11506382-11506755	HepG2	liver:	n/a	n/a
15	CEBPZ	chr2:11506189-11506692	HepG2	liver:	n/a	n/a
16	CEBPB	chr2:11506413-11506843	HepG2	liver:	n/a	chr2:11506637-11506648
17	MYBL2	chr2:11502990-11507033	HepG2	liver:	n/a	n/a
18	MAZ	chr2:11506352-11506691	HepG2	liver:	n/a	n/a
19	CEBPB	chr2:11506335-11506823	HepG2	liver:	n/a	chr2:11506637-11506648
20	ELF1	chr2:11506450-11506848	HepG2	liver:	n/a	n/a
21	FOXA1	chr2:11506353-11506833	HepG2	liver:	n/a	n/a
22	JUND	chr2:11506363-11506648	HepG2	liver:	n/a	n/a
23	MXI1	chr2:11506366-11506808	HepG2	liver:	n/a	n/a
24	SP1	chr2:11506306-11506935	HepG2	liver:	n/a	n/a
25	JUND	chr2:11506403-11506764	HepG2	liver:	n/a	n/a
26	FOXA2	chr2:11505935-11506997	HepG2	liver:	n/a	n/a
27	EP300	chr2:11506425-11506807	HepG2	liver:	n/a	chr2:11506436-11506450 chr2:11506523-11506530
28	CEBPD	chr2:11506389-11506748	HepG2	liver:	n/a	n/a
29	EP300	chr2:11506259-11506840	HepG2	liver:	n/a	chr2:11506436-11506450 chr2:11506523-11506530
30	USF1	chr2:11506441-11506743	HepG2	liver:	n/a	n/a
31	MAX	chr2:11506296-11506916	HepG2	liver:	n/a	n/a
32	TCF7L2	chr2:11506181-11506752	HepG2	liver:	n/a	n/a
33	HEY1	chr2:11506346-11506839	HepG2	liver:	n/a	n/a
34	RAD21	chr2:11506340-11506760	HepG2	liver:	n/a	n/a
35	EP300	chr2:11506253-11506914	HepG2	liver:	n/a	chr2:11506436-11506450 chr2:11506523-11506530
36	ZNF384	chr2:11506521-11506706	K562	blood:	n/a	n/a
37	MAX	chr2:11506221-11507023	HepG2	liver:	n/a	n/a
38	TEAD4	chr2:11505279-11506931	HepG2	liver:	n/a	n/a
39	HDAC2	chr2:11506342-11506886	HepG2	liver:	n/a	n/a
40	HNF4A	chr2:11506410-11506797	HepG2	liver:	n/a	n/a
41	RAD21	chr2:11506328-11506690	HepG2	liver:	n/a	n/a
42	NFIC	chr2:11506340-11506846	HepG2	liver:	n/a	n/a
43	CEBPD	chr2:11506432-11506829	HepG2	liver:	n/a	n/a
44	SMC3	chr2:11505080-11506760	HepG2	liver:	n/a	n/a
45	CEBPB	chr2:11506492-11506742	Hela-S3	cervix:	n/a	chr2:11506637-11506648
46	NFIC	chr2:11506262-11506925	HepG2	liver:	n/a	n/a
47	RXRA	chr2:11506395-11506868	HepG2	liver:	n/a	n/a
48	CEBPB	chr2:11506459-11506866	MCF-7	breast:	n/a	chr2:11506637-11506648
49	MAX	chr2:11506390-11506799	HepG2	liver:	n/a	n/a
50	HNF4A	chr2:11506361-11506823	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:11483340..11487694-chr2:11505828..11510815,5	K562	blood:
2	chr2:11506369..11508414-chr2:11509960..11513532,3	K562	blood:
3	chr2:11502724..11505633-chr2:11505790..11508071,2	K562	blood:

Variant related genes	Relation type
ENSG00000230952	TF binding region
ENSG00000134318	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10170598	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10170791	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10182588	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10195908	0.92[ASN][1000 genomes]
rs10202323	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10929734	0.82[JPT][hapmap]
rs12692438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12692439	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12692440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12692441	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13024110	0.94[CHB][hapmap];0.82[JPT][hapmap];1.00[ASN][1000 genomes]
rs35029584	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4280434	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs4533449	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4641909	0.99[ASN][1000 genomes]
rs4668722	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4668723	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6432189	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6708718	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708945	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6711409	1.00[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs6711414	1.00[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs6716724	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6719739	0.92[ASN][1000 genomes]
rs6721881	1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs6756145	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7420679	0.92[ASN][1000 genomes]
rs7581184	0.86[JPT][hapmap]
rs7595700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12993210	ROCK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11497600-11507400	Weak transcription	Fetal Brain Female	brain
2	chr2:11498200-11507400	Weak transcription	Small Intestine	intestine
3	chr2:11498200-11508000	Weak transcription	Right Atrium	heart
4	chr2:11500000-11507600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:11500200-11507600	Weak transcription	Brain Germinal Matrix	brain
6	chr2:11500400-11507400	Weak transcription	Fetal Lung	lung
7	chr2:11503200-11508000	Weak transcription	Osteobl	bone
8	chr2:11503400-11507400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:11503400-11507800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:11503400-11508000	Weak transcription	Hela-S3	cervix
11	chr2:11504600-11508000	Weak transcription	Psoas Muscle	Psoas
12	chr2:11504800-11507600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr2:11505400-11506800	Flanking Active TSS	HepG2	liver
14	chr2:11505400-11508200	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr2:11505400-11514400	Enhancers	Fetal Intestine Large	intestine
16	chr2:11505600-11507800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:11505600-11508000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:11505600-11511600	Enhancers	Fetal Intestine Small	intestine
19	chr2:11505800-11507400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr2:11505800-11507600	Enhancers	Fetal Brain Male	brain
21	chr2:11505800-11507800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr2:11505800-11508200	Weak transcription	HSMMtube	muscle
23	chr2:11505800-11508200	Weak transcription	NHLF	lung
24	chr2:11505800-11511000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:11506000-11507400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:11506000-11507400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr2:11506000-11507400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr2:11506000-11507400	Weak transcription	HSMM	muscle
29	chr2:11506000-11507800	Weak transcription	Fetal Stomach	stomach
30	chr2:11506000-11508000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr2:11506000-11508200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:11506000-11508200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr2:11506000-11508200	Weak transcription	Fetal Muscle Leg	muscle
34	chr2:11506000-11508200	Weak transcription	Placenta	Placenta
35	chr2:11506000-11508400	Weak transcription	Left Ventricle	heart
36	chr2:11506000-11509000	Weak transcription	Lung	lung
37	chr2:11506000-11509400	Weak transcription	Spleen	Spleen
38	chr2:11506000-11511000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:11506000-11514600	Weak transcription	K562	blood
40	chr2:11506200-11507400	Weak transcription	Liver	Liver
41	chr2:11506200-11507800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:11506200-11507800	Weak transcription	A549	lung
43	chr2:11506200-11508000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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