Variant report

Variant	rs3775068
Chromosome Location	chr4:2888441-2888442
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	RAD21	chr4:2888366-2888710	SK-N-SH_RA	brain:	n/a	n/a
2	POLR2A	chr4:2888289-2888750	SK-N-SH	brain:	n/a	n/a
3	REST	chr4:2888415-2888723	SK-N-SH	brain:	n/a	n/a
4	PBX3	chr4:2888245-2888732	SK-N-SH	brain:	n/a	n/a
5	GATA2	chr4:2888132-2889494	SH-SY5Y	brain:	n/a	chr4:2888583-2888596
6	POLR2A	chr4:2888379-2888808	H1-neurons	neurons:	n/a	n/a
7	EP300	chr4:2888326-2888700	SK-N-SH_RA	brain:	n/a	n/a
8	TCF12	chr4:2888216-2888934	SK-N-SH	brain:	n/a	n/a
9	PBX3	chr4:2888281-2888735	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr4:2888273-2888836	H1-neurons	neurons:	n/a	n/a
11	POLR2A	chr4:2888431-2888675	SK-N-SH	brain:	n/a	n/a
12	TCF12	chr4:2888176-2888912	SK-N-SH	brain:	n/a	n/a
13	EP300	chr4:2888358-2888754	SK-N-SH_RA	brain:	n/a	chr4:2888703-2888713
14	EP300	chr4:2887647-2889416	SK-N-SH	brain:	n/a	chr4:2888847-2888861 chr4:2888703-2888713
15	SIN3AK20	chr4:2888320-2888688	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:2886753..2889164-chr4:2933435..2935256,2	MCF-7	breast:
2	chr4:2887075..2889687-chr4:2908396..2910139,2	MCF-7	breast:
3	chr4:2844115..2846384-chr4:2886095..2888636,2	K562	blood:

Variant related genes	Relation type
ADD1	TF binding region
ENSG00000087274	Chromatin interaction
ENSG00000109736	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1012365	0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs1242228	0.80[GIH][hapmap];0.86[AMR][1000 genomes]
rs1263341	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1263343	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1263345	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs1263347	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs1263349	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs1263359	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1263360	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12648249	0.82[ASN][1000 genomes]
rs13140733	0.83[ASN][1000 genomes]
rs1419045	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs16843452	0.91[CHB][hapmap];0.89[CHD][hapmap]
rs16843523	0.87[CHB][hapmap];0.89[CHD][hapmap];0.81[ASN][1000 genomes]
rs1877723	0.82[YRI][hapmap]
rs2004973	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2051560	0.91[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs2071695	0.91[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs2097081	0.91[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2185885	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs2237004	0.83[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs2239728	0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs2282772	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2282774	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2285084	0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs2798287	0.84[ASN][1000 genomes]
rs3775067	0.94[ASW][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs3796469	0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4690001	0.95[CHB][hapmap];0.89[CHD][hapmap]
rs4690004	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4690005	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4961	1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs4964	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs73082333	0.81[ASN][1000 genomes]
rs73189458	0.80[ASN][1000 genomes]
rs762847	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.92[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	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription 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 miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3775068	GRK4	cis	cerebellum	SCAN
rs3775068	NOP14	cis	cerebellum	SCAN
rs3775068	RNF4	cis	cerebellum	SCAN
rs3775068	MAN2B2	cis	cerebellum	SCAN
rs3775068	ZNF732	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2870200-2914000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:2871200-2896000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:2871200-2900600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:2872200-2890800	Weak transcription	A549	lung
5	chr4:2874200-2900000	Weak transcription	Hela-S3	cervix
6	chr4:2876400-2891600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:2876600-2889600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr4:2876600-2919200	Strong transcription	Primary B cells from peripheral blood	blood
9	chr4:2876800-2889000	Strong transcription	GM12878-XiMat	blood
10	chr4:2876800-2889400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr4:2876800-2891800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:2877000-2889800	Strong transcription	Dnd41	blood
13	chr4:2877200-2891800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:2877200-2919400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:2877400-2889600	Strong transcription	Liver	Liver
16	chr4:2877400-2889600	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr4:2877400-2890000	Strong transcription	Fetal Thymus	thymus
18	chr4:2877400-2890200	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr4:2877400-2891800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr4:2877600-2889600	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr4:2877600-2891400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:2877600-2891600	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr4:2877800-2890800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr4:2877800-2891600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr4:2878000-2891200	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr4:2879000-2889800	Strong transcription	Primary B cells from cord blood	blood
27	chr4:2880200-2889600	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr4:2880600-2889600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr4:2880600-2915000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr4:2881000-2889000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:2881000-2895600	Weak transcription	Right Atrium	heart
32	chr4:2881400-2889400	Strong transcription	Stomach Smooth Muscle	stomach
33	chr4:2882200-2891400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:2883000-2892400	Strong transcription	Fetal Intestine Small	intestine
35	chr4:2883200-2890000	Strong transcription	Thymus	Thymus
36	chr4:2883200-2891000	Strong transcription	Fetal Intestine Large	intestine
37	chr4:2883200-2891600	Strong transcription	Fetal Lung	lung
38	chr4:2883200-2891800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr4:2883400-2888600	Strong transcription	Fetal Brain Female	brain
40	chr4:2883400-2889600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr4:2883400-2890000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr4:2883400-2891400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr4:2883400-2891800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:2883600-2889000	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr4:2883600-2889200	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr4:2883600-2889600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr4:2883600-2889600	Strong transcription	Spleen	Spleen
48	chr4:2883600-2889600	Strong transcription	HepG2	liver
49	chr4:2883600-2889800	Strong transcription	Adipose Nuclei	Adipose
50	chr4:2883600-2890000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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