Variant report

Variant	rs416803
Chromosome Location	chr6:5177038-5177039
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5122792..5124780-chr6:5175533..5177529,2	K562	blood:

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1055415	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12206736	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1535041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1570085	1.00[JPT][hapmap]
rs17139748	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1884976	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1970010	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2145372	1.00[JPT][hapmap]
rs2224391	1.00[JPT][hapmap]
rs2746220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2746221	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2746222	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2746224	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2746226	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2746243	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2753214	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2753230	1.00[JPT][hapmap]
rs2753235	1.00[JPT][hapmap]
rs2753237	1.00[JPT][hapmap]
rs2753238	1.00[JPT][hapmap]
rs2753239	1.00[JPT][hapmap]
rs2753244	1.00[JPT][hapmap]
rs2753245	1.00[JPT][hapmap]
rs2753246	1.00[JPT][hapmap]
rs2753248	1.00[JPT][hapmap]
rs2753255	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2773287	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2773289	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2773291	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2773294	0.91[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2773296	0.91[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes]
rs2773311	1.00[JPT][hapmap]
rs2773314	1.00[JPT][hapmap]
rs2773316	1.00[JPT][hapmap]
rs2773317	1.00[JPT][hapmap]
rs2773318	1.00[JPT][hapmap]
rs2773319	1.00[JPT][hapmap]
rs2773333	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2773335	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2773336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2773337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2773339	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35943326	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs367803	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs374253	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs391313	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs393391	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs393454	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs399283	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs409295	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs419778	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs421186	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs421720	0.91[CEU][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4246073	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs429031	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs429490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs434450	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs439356	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs445711	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs447604	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4960073	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4960074	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs761359	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs761360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs761361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7763280	0.89[LWK][hapmap]
rs9328289	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9378943	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9392664	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9392665	0.87[CEU][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs9405807	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9405809	0.95[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9504356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9504370	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1017821	chr6:5114609-5213200	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
9	nsv538114	chr6:5114609-5213200	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1030254	chr6:5132261-5431585	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
11	nsv1034463	chr6:5137959-5345678	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
12	nsv1022336	chr6:5145194-5200687	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
13	nsv1018984	chr6:5145194-5200801	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1021646	chr6:5157795-5367254	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv538115	chr6:5157795-5367254	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs416803	LYRM4	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5145400-5180800	Weak transcription	Fetal Intestine Small	intestine
2	chr6:5153200-5178200	Weak transcription	HMEC	breast
3	chr6:5163800-5177600	Weak transcription	Aorta	Aorta
4	chr6:5163800-5189600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:5170400-5181800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:5173000-5185400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:5173000-5190800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:5173200-5186000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:5173600-5181000	Weak transcription	NHEK	skin
10	chr6:5173800-5179800	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr6:5174000-5179800	Enhancers	Fetal Thymus	thymus
12	chr6:5174000-5181000	Weak transcription	Pancreas	Pancrea
13	chr6:5174800-5180600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:5175200-5179000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr6:5175400-5177400	Strong transcription	HepG2	liver
16	chr6:5175400-5177800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:5175400-5178000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr6:5175400-5178800	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr6:5175400-5179800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:5175400-5180600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr6:5175400-5181000	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr6:5175600-5177600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:5175600-5179000	Enhancers	Primary T cells from cord blood	blood
24	chr6:5175600-5179600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr6:5175600-5179600	Weak transcription	HUVEC	blood vessel
26	chr6:5175600-5182000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr6:5175600-5185800	Weak transcription	Fetal Stomach	stomach
28	chr6:5175800-5178200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:5175800-5180000	Weak transcription	Brain Angular Gyrus	brain
30	chr6:5175800-5180000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr6:5175800-5180000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr6:5175800-5180800	Weak transcription	Esophagus	oesophagus
33	chr6:5175800-5193400	Weak transcription	Brain Substantia Nigra	brain
34	chr6:5176000-5179200	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr6:5176200-5177400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:5176200-5177600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:5176200-5177600	Enhancers	GM12878-XiMat	blood
38	chr6:5176200-5178000	Weak transcription	Fetal Brain Female	brain
39	chr6:5176200-5178400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr6:5176200-5178600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:5176200-5178800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:5176200-5180000	Weak transcription	Brain Anterior Caudate	brain
43	chr6:5176200-5180200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr6:5176200-5180400	Weak transcription	Placenta	Placenta
45	chr6:5176200-5181400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr6:5176200-5181400	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr6:5176200-5181800	Weak transcription	Left Ventricle	heart
48	chr6:5176200-5181800	Weak transcription	Spleen	Spleen
49	chr6:5176200-5183800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr6:5176200-5190600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links