Variant report

Variant	rs630379
Chromosome Location	chr6:31922254-31922255
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:31914529-31923123	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:31922048-31922496	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:31921988-31922463	HepG2	liver:	n/a	n/a
4	POLR2A	chr6:31912538-31923721	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31862879..31872535-chr6:31911667..31928766,47	MCF-7	breast:
2	chr6:31864040..31872511-chr6:31917614..31930102,27	MCF-7	breast:
3	chr6:31800897..31803228-chr6:31920602..31922678,3	MCF-7	breast:
4	chr6:31795636..31798245-chr6:31918876..31922534,3	MCF-7	breast:
5	chr6:31837066..31839045-chr6:31922002..31924631,2	K562	blood:

No data

Variant related genes	Relation type
SKIV2L	TF binding region
ENSG00000204385	Chromatin interaction
ENSG00000204366	Chromatin interaction
ENSG00000204387	Chromatin interaction
ENSG00000166278	Chromatin interaction
ENSG00000204371	Chromatin interaction
ENSG00000204388	Chromatin interaction
ENSG00000201823	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1048709	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs386480	0.96[EUR][1000 genomes]
rs389883	0.96[EUR][1000 genomes]
rs410851	0.97[EUR][1000 genomes]
rs419788	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs437179	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs440454	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs537160	0.82[AMR][1000 genomes];0.82[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs630379	HMGA1	cis	cerebellum	SCAN
rs630379	HLA-DRB5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31914200-31926000	Weak transcription	Right Atrium	heart
2	chr6:31914800-31922400	Weak transcription	Stomach Mucosa	stomach
3	chr6:31917000-31925000	Strong transcription	Spleen	Spleen
4	chr6:31917600-31922400	Strong transcription	Fetal Thymus	thymus
5	chr6:31917600-31925000	Strong transcription	Lung	lung
6	chr6:31917600-31925600	Weak transcription	Fetal Heart	heart
7	chr6:31917800-31925000	Strong transcription	NHLF	lung
8	chr6:31917800-31925200	Strong transcription	A549	lung
9	chr6:31917800-31925400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:31917800-31925400	Strong transcription	Primary T cells from cord blood	blood
11	chr6:31918000-31923400	Strong transcription	Gastric	stomach
12	chr6:31918000-31924400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr6:31918000-31925000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:31918000-31925000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:31918000-31925000	Strong transcription	Fetal Intestine Small	intestine
16	chr6:31918000-31925200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:31918000-31925200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:31918200-31923200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:31918200-31924600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr6:31918200-31924800	Strong transcription	Pancreas	Pancrea
21	chr6:31918200-31925000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr6:31918200-31925000	Strong transcription	Fetal Stomach	stomach
23	chr6:31918200-31925000	Strong transcription	Stomach Smooth Muscle	stomach
24	chr6:31918200-31925400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:31918400-31924400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr6:31918400-31924400	Strong transcription	Liver	Liver
27	chr6:31918400-31924600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:31918400-31925000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:31918400-31925000	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr6:31918400-31925000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:31918400-31925000	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr6:31918400-31925000	Strong transcription	Brain Germinal Matrix	brain
33	chr6:31918400-31925000	Strong transcription	Brain Substantia Nigra	brain
34	chr6:31918400-31925000	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr6:31918400-31925200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:31918400-31925200	Strong transcription	Duodenum Mucosa	Duodenum
37	chr6:31918400-31925400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr6:31918600-31922400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:31918600-31924800	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr6:31918600-31924800	Strong transcription	Thymus	Thymus
41	chr6:31918600-31925000	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr6:31918600-31925000	Strong transcription	Brain Angular Gyrus	brain
43	chr6:31918600-31925000	Strong transcription	Brain Anterior Caudate	brain
44	chr6:31918600-31925000	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr6:31918600-31925200	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr6:31918600-31925200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr6:31918600-31925200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:31918600-31925200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:31918600-31925200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:31918600-31925200	Strong transcription	Brain Hippocampus Middle	brain

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