Variant report

Variant	rs550513
Chromosome Location	chr6:31920687-31920688
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31648483..31649141-chr6:31920167..31920748,3	K562	blood:
2	chr6:31862879..31872535-chr6:31911667..31928766,47	MCF-7	breast:
3	chr6:31864040..31872511-chr6:31917614..31930102,27	MCF-7	breast:
4	chr6:31865036..31866364-chr6:31919851..31920783,4	MCF-7	breast:
5	chr6:31800897..31803228-chr6:31920602..31922678,3	MCF-7	breast:
6	chr6:31801272..31804221-chr6:31918478..31920926,2	K562	blood:
7	chr6:31890425..31891402-chr6:31919829..31921030,3	MCF-7	breast:
8	chr6:31869929..31870848-chr6:31919914..31920759,2	MCF-7	breast:
9	chr6:31869703..31871388-chr6:31919073..31921188,2	K562	blood:
10	chr6:31795636..31798245-chr6:31918876..31922534,3	MCF-7	breast:
11	chr6:31903526..31904127-chr6:31919858..31920693,2	MCF-7	breast:
12	chr6:31864115..31868338-chr6:31917147..31921993,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000204388	Chromatin interaction
ENSG00000204366	Chromatin interaction
ENSG00000204387	Chromatin interaction
ENSG00000201823	Chromatin interaction
ENSG00000166278	Chromatin interaction
ENSG00000204371	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1042663	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2072634	0.86[ASN][1000 genomes]
rs2507953	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs403569	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs438999	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs522162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs547154	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs550605	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs641153	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs653414	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs654727	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7754520	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7772063	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
2	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
3	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
5	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
7	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
9	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
10	nsv601950	chr6:31785438-32492308	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	197 gene(s)	inside rSNPs	diseases
11	nsv601951	chr6:31785438-32496748	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	197 gene(s)	inside rSNPs	diseases
12	nsv601955	chr6:31785453-32484368	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
13	nsv601956	chr6:31785453-32492308	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	197 gene(s)	inside rSNPs	diseases
14	nsv601961	chr6:31868322-32484368	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
15	nsv427751	chr6:31871512-32092843	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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 miRNA target site	91 gene(s)	inside rSNPs	diseases
16	nsv428141	chr6:31871512-32092843	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
17	esv2758043	chr6:31871512-32209113	Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
18	esv2759415	chr6:31871512-32209113	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
19	nsv830628	chr6:31887554-31947600	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
20	nsv933250	chr6:31905060-32008005	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
21	nsv934279	chr6:31905060-32013902	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
22	nsv884512	chr6:31908470-31933161	Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs550513	SKIV2L	cis	Adipose Subcutaneous	GTEx
rs550513	SKIV2L	cis	Esophagus Muscularis	GTEx
rs550513	SKIV2L	cis	multi-tissue	Pritchard
rs550513	LEMD2	cis	parietal	SCAN
rs550513	RDBP	cis	lymphoblastoid	seeQTL
rs550513	SKIV2L	cis	Skin Sun Exposed Lower leg	GTEx
rs550513	ITPR3	cis	parietal	SCAN
rs550513	RDBP	cis	multi-tissue	Pritchard
rs550513	SKIV2L	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31913200-31920800	Weak transcription	Small Intestine	intestine
2	chr6:31914200-31926000	Weak transcription	Right Atrium	heart
3	chr6:31914800-31922400	Weak transcription	Stomach Mucosa	stomach
4	chr6:31917000-31925000	Strong transcription	Spleen	Spleen
5	chr6:31917200-31921400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:31917600-31921000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr6:31917600-31922400	Strong transcription	Fetal Thymus	thymus
8	chr6:31917600-31925000	Strong transcription	Lung	lung
9	chr6:31917600-31925600	Weak transcription	Fetal Heart	heart
10	chr6:31917800-31925000	Strong transcription	NHLF	lung
11	chr6:31917800-31925200	Strong transcription	A549	lung
12	chr6:31917800-31925400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:31917800-31925400	Strong transcription	Primary T cells from cord blood	blood
14	chr6:31918000-31923400	Strong transcription	Gastric	stomach
15	chr6:31918000-31924400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:31918000-31925000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:31918000-31925000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:31918000-31925000	Strong transcription	Fetal Intestine Small	intestine
19	chr6:31918000-31925200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:31918000-31925200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:31918200-31921800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr6:31918200-31923200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:31918200-31924600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr6:31918200-31924800	Strong transcription	Pancreas	Pancrea
25	chr6:31918200-31925000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:31918200-31925000	Strong transcription	Fetal Stomach	stomach
27	chr6:31918200-31925000	Strong transcription	Stomach Smooth Muscle	stomach
28	chr6:31918200-31925400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:31918400-31922000	Weak transcription	Psoas Muscle	Psoas
30	chr6:31918400-31924400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:31918400-31924400	Strong transcription	Liver	Liver
32	chr6:31918400-31924600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:31918400-31925000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:31918400-31925000	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr6:31918400-31925000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:31918400-31925000	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr6:31918400-31925000	Strong transcription	Brain Germinal Matrix	brain
38	chr6:31918400-31925000	Strong transcription	Brain Substantia Nigra	brain
39	chr6:31918400-31925000	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr6:31918400-31925200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:31918400-31925200	Strong transcription	Duodenum Mucosa	Duodenum
42	chr6:31918400-31925400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr6:31918600-31922400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr6:31918600-31924800	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr6:31918600-31924800	Strong transcription	Thymus	Thymus
46	chr6:31918600-31925000	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr6:31918600-31925000	Strong transcription	Brain Angular Gyrus	brain
48	chr6:31918600-31925000	Strong transcription	Brain Anterior Caudate	brain
49	chr6:31918600-31925000	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr6:31918600-31925200	Strong transcription	HUES6 Cell Line	embryonic stem cell

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