Variant report

Variant	rs12990641
Chromosome Location	chr2:11506043-11506044
allele	A/G
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	EP300	chr2:11505142-11506108	HepG2	liver:	n/a	n/a
2	MBD4	chr2:11504977-11506100	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:11503590-11506128	HepG2	liver:	n/a	n/a
4	MXI1	chr2:11505177-11506052	HepG2	liver:	n/a	n/a
5	CEBPD	chr2:11505326-11506109	HepG2	liver:	n/a	n/a
6	REST	chr2:11505147-11506101	HepG2	liver:	n/a	chr2:11505845-11505858 chr2:11505918-11505931 chr2:11505858-11505866
7	MAFK	chr2:11505289-11506093	HepG2	liver:	n/a	n/a
8	MAX	chr2:11505066-11506178	HepG2	liver:	n/a	chr2:11505914-11505924
9	ARID3A	chr2:11505103-11506863	HepG2	liver:	n/a	n/a
10	MAZ	chr2:11505282-11506090	HepG2	liver:	n/a	chr2:11505914-11505924
11	MYBL2	chr2:11502990-11507033	HepG2	liver:	n/a	n/a
12	JUND	chr2:11505472-11506152	HepG2	liver:	n/a	chr2:11505971-11505983
13	POLR2A	chr2:11506026-11506237	K562	blood:	n/a	n/a
14	NFIC	chr2:11505336-11506059	HepG2	liver:	n/a	n/a
15	FOXA2	chr2:11505935-11506997	HepG2	liver:	n/a	n/a
16	EP300	chr2:11505262-11506056	HepG2	liver:	n/a	n/a
17	TEAD4	chr2:11505279-11506931	HepG2	liver:	n/a	n/a
18	MYBL2	chr2:11504668-11506224	HepG2	liver:	n/a	n/a
19	HEY1	chr2:11502991-11506146	HepG2	liver:	n/a	n/a
20	SMC3	chr2:11505080-11506760	HepG2	liver:	n/a	n/a
21	POLR2A	chr2:11502460-11506090	HepG2	liver:	n/a	n/a
22	MBD4	chr2:11504774-11506851	HepG2	liver:	n/a	n/a
23	NFIC	chr2:11505063-11506116	HepG2	liver:	n/a	n/a
24	TBP	chr2:11505044-11506088	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11483340..11487694-chr2:11505828..11510815,5	K562	blood:
2	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: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10178332	0.81[CEU][hapmap]
rs10192994	0.80[CEU][hapmap]
rs10194620	0.84[CEU][hapmap]
rs10201229	1.00[JPT][hapmap]
rs10203916	0.87[CEU][hapmap]
rs10205944	0.87[CEU][hapmap]
rs10210600	0.85[CEU][hapmap]
rs10454126	0.87[CEU][hapmap]
rs11694729	0.87[CEU][hapmap]
rs11695377	0.87[CEU][hapmap]
rs12621519	1.00[JPT][hapmap]
rs12692434	0.86[CEU][hapmap]
rs12692437	0.86[CEU][hapmap]
rs12997263	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13015560	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13017021	1.00[CEU][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13020022	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1562748	0.87[CEU][hapmap]
rs1562749	0.93[CEU][hapmap]
rs1868584	0.93[CEU][hapmap]
rs2044758	0.93[CEU][hapmap]
rs2084577	0.87[CEU][hapmap]
rs2357996	0.93[CEU][hapmap]
rs34760292	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34887515	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35231136	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35665018	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35750432	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3911110	0.87[CEU][hapmap]
rs4303693	0.81[CEU][hapmap]
rs4669710	0.87[CEU][hapmap]
rs4669713	0.87[CEU][hapmap]
rs4669715	0.93[CEU][hapmap]
rs6432183	0.93[CEU][hapmap]
rs6432184	0.93[CEU][hapmap]
rs6432186	0.87[CEU][hapmap]
rs6713273	0.87[CEU][hapmap]
rs6721445	0.87[CEU][hapmap]
rs6733312	0.86[CEU][hapmap]
rs6749456	0.87[CEU][hapmap]
rs6755196	0.87[CEU][hapmap]
rs6760802	0.93[CEU][hapmap]
rs71439056	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71439057	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7355446	0.86[CEU][hapmap]
rs753770	0.87[CEU][hapmap]
rs7563928	0.86[CEU][hapmap]
rs7593091	0.87[CEU][hapmap]
rs9287728	0.93[CEU][hapmap]
rs965665	0.93[CEU][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12990641	ROCK2	cis	cerebellum	SCAN
rs12990641	IAH1	cis	cerebellum	SCAN
rs12990641	PQLC3	Cis_1M	lymphoblastoid	RTeQTL
rs12990641	CD3D	trans	lymphoblastoid	seeQTL
rs12990641	ROCK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 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	chr2:11505200-11506200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:11505400-11506200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:11505400-11506200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:11505400-11506200	Enhancers	Liver	Liver
17	chr2:11505400-11506800	Flanking Active TSS	HepG2	liver
18	chr2:11505400-11508200	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr2:11505400-11514400	Enhancers	Fetal Intestine Large	intestine
20	chr2:11505600-11506200	Enhancers	A549	lung
21	chr2:11505600-11507800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:11505600-11508000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:11505600-11511600	Enhancers	Fetal Intestine Small	intestine
24	chr2:11505800-11507400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:11505800-11507600	Enhancers	Fetal Brain Male	brain
26	chr2:11505800-11507800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr2:11505800-11508200	Weak transcription	HSMMtube	muscle
28	chr2:11505800-11508200	Weak transcription	NHLF	lung
29	chr2:11505800-11511000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:11506000-11507400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:11506000-11507400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr2:11506000-11507400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr2:11506000-11507400	Weak transcription	HSMM	muscle
34	chr2:11506000-11507800	Weak transcription	Fetal Stomach	stomach
35	chr2:11506000-11508000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr2:11506000-11508200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:11506000-11508200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr2:11506000-11508200	Weak transcription	Fetal Muscle Leg	muscle
39	chr2:11506000-11508200	Weak transcription	Placenta	Placenta
40	chr2:11506000-11508400	Weak transcription	Left Ventricle	heart
41	chr2:11506000-11509000	Weak transcription	Lung	lung
42	chr2:11506000-11509400	Weak transcription	Spleen	Spleen
43	chr2:11506000-11511000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:11506000-11514600	Weak transcription	K562	blood

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