Variant report

Variant	rs6600769
Chromosome Location	chr4:2856235-2856236
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:2855740..2858209-chr4:2858751..2860482,2	K562	blood:
2	chr4:2855341..2858315-chr4:2935063..2937111,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109736	Chromatin interaction
ENSG00000249673	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10026792	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]
rs1014947	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1014948	0.82[EUR][1000 genomes]
rs12623	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1263412	0.83[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12641947	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12643323	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12647647	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12647713	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12649553	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16843589	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16843603	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs17833172	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17833250	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17833981	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17834203	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1877723	0.83[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2032470	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2096760	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3021131	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35780153	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55927173	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58115360	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59150074	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs624833	0.83[CEU][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6819310	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6824567	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7436306	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7655104	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7678161	0.83[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878444	chr4:2689449-2861090	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv878450	chr4:2760222-2861090	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	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
6	nsv878451	chr4:2785556-2856687	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv526059	chr4:2850142-2861090	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	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
rs6600769	CYTL1	cis	parietal	SCAN
rs6600769	RNF4	cis	cerebellum	SCAN
rs6600769	LRPAP1	cis	cerebellum	SCAN
rs6600769	GRK4	cis	cerebellum	SCAN
rs6600769	GRK4	cis	Thyroid	GTEx
rs6600769	GRK4	cis	Artery Tibial	GTEx
rs6600769	ADD1	cis	multi-tissue	Pritchard
rs6600769	GRK4	cis	Skin Sun Exposed Lower leg	GTEx
rs6600769	TETRAN	cis	multi-tissue	Pritchard
rs6600769	LRPAP1	cis	parietal	SCAN
rs6600769	NOP14	cis	cerebellum	SCAN
rs6600769	GRK4	cis	Artery Aorta	GTEx
rs6600769	STX18	cis	parietal	SCAN

Chromatin state (count:123 , 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	chr4:2846800-2857400	Weak transcription	Aorta	Aorta
3	chr4:2846800-2861800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:2846800-2861800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:2846800-2862000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:2846800-2862600	Weak transcription	Esophagus	oesophagus
7	chr4:2847200-2862200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr4:2847400-2859800	Weak transcription	A549	lung
9	chr4:2847400-2863600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:2848000-2861200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr4:2850000-2860400	Weak transcription	Fetal Brain Male	brain
12	chr4:2850400-2856400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:2851000-2860000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr4:2851400-2857400	Weak transcription	Pancreas	Pancrea
15	chr4:2852000-2860200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:2852000-2865800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:2852600-2858200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr4:2853400-2859800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:2853400-2860000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:2853400-2861200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr4:2853400-2861400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr4:2854200-2857000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:2854400-2859800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:2854600-2856600	Weak transcription	Psoas Muscle	Psoas
25	chr4:2854600-2856800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:2854600-2857000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:2854600-2857000	Strong transcription	Dnd41	blood
28	chr4:2854600-2857600	Weak transcription	Right Atrium	heart
29	chr4:2854600-2858400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:2854800-2856400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:2854800-2856600	Enhancers	Primary T cells from cord blood	blood
32	chr4:2854800-2856600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:2854800-2857000	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr4:2854800-2857200	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr4:2854800-2857400	Weak transcription	Brain Substantia Nigra	brain
36	chr4:2854800-2860200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:2854800-2862000	Weak transcription	NHEK	skin
38	chr4:2854800-2862800	Weak transcription	Gastric	stomach
39	chr4:2855000-2857000	Strong transcription	Fetal Brain Female	brain
40	chr4:2855000-2858200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr4:2855000-2859400	Weak transcription	NHLF	lung
42	chr4:2855000-2859600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr4:2855000-2860000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr4:2855000-2860000	Weak transcription	Stomach Mucosa	stomach
45	chr4:2855000-2863000	Genic enhancers	Primary B cells from peripheral blood	blood
46	chr4:2855000-2863400	Weak transcription	Brain Angular Gyrus	brain
47	chr4:2855200-2856800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr4:2855200-2857000	Genic enhancers	Duodenum Mucosa	Duodenum
49	chr4:2855200-2859400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr4:2855200-2860400	Strong transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links