Variant report

Variant	rs624833
Chromosome Location	chr4:2881256-2881257
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:2879534..2882793-chr4:2935370..2940285,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249673	Chromatin interaction
ENSG00000109736	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10026792	0.91[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1014947	0.83[CEU][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[ASN][1000 genomes]
rs1014948	0.83[ASN][1000 genomes]
rs12623	0.82[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1263412	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12641947	0.92[ASN][1000 genomes]
rs12643323	0.83[ASN][1000 genomes]
rs12647647	0.83[ASN][1000 genomes]
rs12647713	0.83[ASN][1000 genomes]
rs12649553	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs16843589	0.83[CEU][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.87[ASN][1000 genomes]
rs16843603	0.83[CEU][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17833172	0.83[CEU][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17833250	0.83[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs17833981	0.83[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.87[ASN][1000 genomes]
rs17834203	0.83[CEU][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[ASN][1000 genomes]
rs1877723	1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2032470	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2096760	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2471324	0.86[CEU][hapmap]
rs3021131	0.83[ASN][1000 genomes]
rs35780153	1.00[JPT][hapmap];0.88[TSI][hapmap];0.95[ASN][1000 genomes]
rs55927173	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58115360	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59150074	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6600769	0.83[CEU][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6819310	0.83[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6824567	0.83[CEU][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7436306	0.83[ASN][1000 genomes]
rs7655104	0.92[ASN][1000 genomes]
rs7678161	1.00[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv593435	chr4:2770772-2881256	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv521858	chr4:2846799-2881256	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv524060	chr4:2850142-2881256	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs624833	LRPAP1	cis	parietal	SCAN
rs624833	GRK4	cis	cerebellum	SCAN
rs624833	RNF4	cis	cerebellum	SCAN
rs624833	NOP14	cis	cerebellum	SCAN
rs624833	GRK4	cis	Skin Sun Exposed Lower leg	GTEx
rs624833	GRK4	cis	Artery Tibial	GTEx
rs624833	GRK4	cis	lung	GTEx
rs624833	GRK4	cis	Thyroid	GTEx
rs624833	GRK4	cis	Artery Aorta	GTEx
rs624833	LOC93622	cis	cerebellum	SCAN
rs624833	GRK4	Cis_1M	lymphoblastoid	RTeQTL
rs624833	CYTL1	cis	parietal	SCAN
rs624833	GRK4	cis	Adipose Subcutaneous	GTEx

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	chr4:2871200-2881600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr4:2871200-2886000	Weak transcription	Aorta	Aorta
6	chr4:2871200-2896000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:2871200-2900600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:2872200-2890800	Weak transcription	A549	lung
9	chr4:2874000-2883600	Weak transcription	NH-A	brain
10	chr4:2874000-2887000	Weak transcription	Fetal Heart	heart
11	chr4:2874200-2900000	Weak transcription	Hela-S3	cervix
12	chr4:2875400-2886000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:2875800-2884200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr4:2876000-2881800	Strong transcription	Fetal Intestine Small	intestine
15	chr4:2876000-2884000	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:2876000-2885800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr4:2876000-2886000	Weak transcription	Colonic Mucosa	Colon
18	chr4:2876000-2886600	Weak transcription	Stomach Mucosa	stomach
19	chr4:2876400-2891600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:2876600-2882600	Strong transcription	Fetal Stomach	stomach
21	chr4:2876600-2889600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr4:2876600-2919200	Strong transcription	Primary B cells from peripheral blood	blood
23	chr4:2876800-2881800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:2876800-2889000	Strong transcription	GM12878-XiMat	blood
25	chr4:2876800-2889400	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr4:2876800-2891800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr4:2877000-2882000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:2877000-2882200	Strong transcription	Fetal Muscle Trunk	muscle
29	chr4:2877000-2883600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr4:2877000-2883800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr4:2877000-2886000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr4:2877000-2889800	Strong transcription	Dnd41	blood
33	chr4:2877200-2882000	Strong transcription	Brain Germinal Matrix	brain
34	chr4:2877200-2882200	Strong transcription	Fetal Muscle Leg	muscle
35	chr4:2877200-2886200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr4:2877200-2891800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:2877200-2919400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:2877400-2882000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr4:2877400-2882000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:2877400-2882000	Strong transcription	Placenta	Placenta
41	chr4:2877400-2882000	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr4:2877400-2882000	Strong transcription	HepG2	liver
43	chr4:2877400-2882200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:2877400-2882400	Strong transcription	Primary hematopoietic stem cells	blood
45	chr4:2877400-2882400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr4:2877400-2882400	Strong transcription	Fetal Intestine Large	intestine
47	chr4:2877400-2882400	Strong transcription	Fetal Lung	lung
48	chr4:2877400-2884000	Weak transcription	Small Intestine	intestine
49	chr4:2877400-2886200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr4:2877400-2889600	Strong transcription	Liver	Liver

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