Variant report

Variant	rs10026792
Chromosome Location	chr4:2862190-2862191
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:2858420..2863571-chr4:2865919..2871146,8	K562	blood:
2	chr4:2844665..2847425-chr4:2860428..2864789,5	MCF-7	breast:
3	chr4:2860130..2862463-chr4:2876073..2878049,2	K562	blood:
4	chr4:2857762..2859404-chr4:2861452..2863344,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000087274	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1014947	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs1014948	0.81[AMR][1000 genomes]
rs1034400	1.00[CHB][hapmap]
rs12623	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs1263412	0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12641947	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12643323	0.81[AMR][1000 genomes]
rs12647647	0.81[AMR][1000 genomes]
rs12647713	0.82[AMR][1000 genomes]
rs12649553	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs16843169	1.00[CHB][hapmap]
rs16843481	1.00[CHB][hapmap]
rs16843535	1.00[CHB][hapmap]
rs16843589	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs16843596	1.00[CHB][hapmap]
rs16843603	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs17833172	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17833250	0.89[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17833981	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes]
rs17834203	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes]
rs1877723	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2032470	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2096760	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs231696	1.00[CHB][hapmap]
rs231706	1.00[CHB][hapmap]
rs2857845	1.00[CHB][hapmap]
rs2858039	1.00[CHB][hapmap]
rs3213502	1.00[CHB][hapmap]
rs35780153	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs41528047	1.00[CHB][hapmap]
rs4690006	1.00[CHB][hapmap]
rs55927173	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs58115360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59150074	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs624833	0.91[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6600769	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6819310	0.91[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6824567	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7655104	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7678161	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];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	nsv1010533	chr4:2792848-2873441	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	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
6	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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs10026792	STX18	cis	parietal	SCAN
rs10026792	RNF4	cis	cerebellum	SCAN
rs10026792	GRK4	cis	cerebellum	SCAN
rs10026792	GRK4	cis	Thyroid	GTEx
rs10026792	PPP2R2C	cis	parietal	SCAN
rs10026792	GRK4	cis	Skin Sun Exposed Lower leg	GTEx
rs10026792	CYTL1	cis	parietal	SCAN
rs10026792	GRK4	cis	Artery Tibial	GTEx
rs10026792	TETRAN	cis	multi-tissue	Pritchard
rs10026792	LRPAP1	cis	parietal	SCAN
rs10026792	LRPAP1	cis	cerebellum	SCAN
rs10026792	ADD1	cis	multi-tissue	Pritchard
rs10026792	NOP14	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2846600-2862400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:2846800-2862600	Weak transcription	Esophagus	oesophagus
3	chr4:2847200-2862200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr4:2847400-2863600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr4:2852000-2865800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:2854800-2862800	Weak transcription	Gastric	stomach
7	chr4:2855000-2863000	Genic enhancers	Primary B cells from peripheral blood	blood
8	chr4:2855000-2863400	Weak transcription	Brain Angular Gyrus	brain
9	chr4:2855200-2862400	Genic enhancers	Primary B cells from cord blood	blood
10	chr4:2856200-2862400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr4:2856400-2862600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:2856600-2862200	Enhancers	HepG2	liver
13	chr4:2856600-2862800	Weak transcription	Brain Germinal Matrix	brain
14	chr4:2856800-2862600	Weak transcription	Thymus	Thymus
15	chr4:2856800-2863800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr4:2857000-2877000	Weak transcription	Dnd41	blood
17	chr4:2857200-2867600	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr4:2857400-2870000	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr4:2857400-2877600	Weak transcription	HMEC	breast
20	chr4:2857600-2867400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr4:2857800-2862800	Weak transcription	Aorta	Aorta
22	chr4:2858200-2864800	Enhancers	Liver	Liver
23	chr4:2858400-2867200	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr4:2858800-2865200	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr4:2859000-2865200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr4:2859000-2865200	Enhancers	Fetal Muscle Leg	muscle
27	chr4:2859200-2862400	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr4:2859200-2862800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr4:2859200-2863400	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr4:2859200-2869400	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr4:2859400-2865000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:2859400-2865000	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr4:2859400-2865400	Enhancers	HSMMtube	muscle
34	chr4:2859400-2865800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr4:2859400-2867200	Enhancers	Small Intestine	intestine
36	chr4:2859600-2862600	Weak transcription	Placenta	Placenta
37	chr4:2859600-2864800	Enhancers	HUVEC	blood vessel
38	chr4:2859600-2865600	Enhancers	Adipose Nuclei	Adipose
39	chr4:2859600-2866000	Enhancers	Duodenum Mucosa	Duodenum
40	chr4:2859800-2864000	Enhancers	NHDF-Ad	bronchial
41	chr4:2859800-2864800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr4:2859800-2865000	Enhancers	Osteobl	bone
43	chr4:2859800-2865400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:2859800-2865600	Enhancers	Fetal Heart	heart
45	chr4:2859800-2866600	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr4:2860000-2862800	Enhancers	Brain Anterior Caudate	brain
47	chr4:2860000-2863400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr4:2860000-2863800	Enhancers	GM12878-XiMat	blood
49	chr4:2860000-2864200	Enhancers	Rectal Smooth Muscle	rectum
50	chr4:2860000-2864600	Enhancers	Fetal Lung	lung

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