Variant report

Variant	rs1242228
Chromosome Location	chr4:2882007-2882008
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:2879534..2882793-chr4:2935370..2940285,4	MCF-7	breast:
2	chr4:2818530..2821169-chr4:2881997..2885134,3	K562	blood:
3	chr4:2868702..2870783-chr4:2881589..2883580,3	K562	blood:

Variant related genes	Relation type
ENSG00000087274	Chromatin interaction
ENSG00000087266	Chromatin interaction
ENSG00000249673	Chromatin interaction
ENSG00000109736	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1012365	0.86[CHB][hapmap]
rs1263343	0.82[EUR][1000 genomes]
rs1263345	0.91[CHB][hapmap]
rs1263347	0.95[CHB][hapmap]
rs1263359	0.83[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1263360	0.81[JPT][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1419045	0.86[CHB][hapmap]
rs16843452	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs16843523	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2004973	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2097081	0.87[CHB][hapmap]
rs2185885	0.86[CHB][hapmap]
rs2239728	0.83[CHB][hapmap]
rs2285084	0.83[CHB][hapmap]
rs3775068	0.80[GIH][hapmap];0.86[AMR][1000 genomes]
rs4690001	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4690004	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4961	0.82[CHB][hapmap]
rs4964	0.95[CHB][hapmap]
rs762847	0.86[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv3383963	chr4:2877954-2882252	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1242228	NOP14	cis	cerebellum	SCAN
rs1242228	RGS12	cis	parietal	SCAN
rs1242228	CPLX1	cis	parietal	SCAN
rs1242228	MAN2B2	cis	cerebellum	SCAN
rs1242228	LRPAP1	cis	cerebellum	SCAN
rs1242228	GRK4	cis	cerebellum	SCAN
rs1242228	RNF4	cis	cerebellum	SCAN
rs1242228	ZNF141	cis	parietal	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	chr4:2870600-2886000	Weak transcription	Fetal Brain Male	brain
3	chr4:2871000-2885800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr4:2871200-2886000	Weak transcription	Aorta	Aorta
5	chr4:2871200-2896000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:2871200-2900600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:2872200-2890800	Weak transcription	A549	lung
8	chr4:2874000-2883600	Weak transcription	NH-A	brain
9	chr4:2874000-2887000	Weak transcription	Fetal Heart	heart
10	chr4:2874200-2900000	Weak transcription	Hela-S3	cervix
11	chr4:2875400-2886000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr4:2875800-2884200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr4:2876000-2884000	Weak transcription	Colon Smooth Muscle	Colon
14	chr4:2876000-2885800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr4:2876000-2886000	Weak transcription	Colonic Mucosa	Colon
16	chr4:2876000-2886600	Weak transcription	Stomach Mucosa	stomach
17	chr4:2876400-2891600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:2876600-2882600	Strong transcription	Fetal Stomach	stomach
19	chr4:2876600-2889600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr4:2876600-2919200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr4:2876800-2889000	Strong transcription	GM12878-XiMat	blood
22	chr4:2876800-2889400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr4:2876800-2891800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr4:2877000-2882200	Strong transcription	Fetal Muscle Trunk	muscle
25	chr4:2877000-2883600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr4:2877000-2883800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr4:2877000-2886000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr4:2877000-2889800	Strong transcription	Dnd41	blood
29	chr4:2877200-2882200	Strong transcription	Fetal Muscle Leg	muscle
30	chr4:2877200-2886200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr4:2877200-2891800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:2877200-2919400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:2877400-2882200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:2877400-2882400	Strong transcription	Primary hematopoietic stem cells	blood
35	chr4:2877400-2882400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr4:2877400-2882400	Strong transcription	Fetal Intestine Large	intestine
37	chr4:2877400-2882400	Strong transcription	Fetal Lung	lung
38	chr4:2877400-2884000	Weak transcription	Small Intestine	intestine
39	chr4:2877400-2886200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:2877400-2889600	Strong transcription	Liver	Liver
41	chr4:2877400-2889600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr4:2877400-2890000	Strong transcription	Fetal Thymus	thymus
43	chr4:2877400-2890200	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr4:2877400-2891800	Strong transcription	Duodenum Mucosa	Duodenum
45	chr4:2877600-2882200	Strong transcription	Primary T cells from cord blood	blood
46	chr4:2877600-2882200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr4:2877600-2884000	Weak transcription	Brain Angular Gyrus	brain
48	chr4:2877600-2889600	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr4:2877600-2891400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:2877600-2891600	Strong transcription	Primary T cells fromperipheralblood	blood

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