Variant report

Variant	rs11964596
Chromosome Location	chr6:30736541-30736542
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30735343..30739242-chr6:30745410..30750382,5	MCF-7	breast:
2	chr6:30735516..30738178-chr6:30794315..30796554,3	MCF-7	breast:
3	chr6:30710566..30712092-chr6:30736043..30738574,2	K562	blood:
4	chr6:30736125..30739794-chr6:30850488..30852740,4	MCF-7	breast:
5	chr6:30736036..30738964-chr6:30760194..30762277,2	K562	blood:
6	chr6:30735613..30737637-chr6:30772309..30773867,2	MCF-7	breast:
7	chr6:30735902..30738522-chr6:30790223..30792279,2	MCF-7	breast:
8	chr6:30718213..30720265-chr6:30735663..30737554,3	K562	blood:
9	chr6:30735539..30738504-chr6:30880365..30881967,2	MCF-7	breast:
10	chr6:30735949..30738859-chr6:30853029..30855349,2	MCF-7	breast:
11	chr6:30734934..30736907-chr6:30848739..30852223,3	MCF-7	breast:
12	chr6:30732229..30734221-chr6:30735941..30738002,2	K562	blood:
13	chr6:30735347..30739906-chr6:30783605..30789456,10	MCF-7	breast:
14	chr6:30735402..30739247-chr6:30785239..30791444,10	MCF-7	breast:
15	chr6:30726903..30729816-chr6:30736090..30739671,3	K562	blood:
16	chr6:30735125..30737471-chr6:30740402..30742755,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000263608	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000228022	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11963870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966040	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095340	0.94[ASN][1000 genomes]
rs35278546	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35826335	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4248148	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription 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	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS 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	967 gene(s)	inside rSNPs	diseases
5	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
6	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	nsv884100	chr6:30693816-30751326	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
8	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
9	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
10	nsv870418	chr6:30713196-30755668	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	nsv527226	chr6:30716719-30772378	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv884103	chr6:30729487-30755668	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11964596	IER3	cis	lymphoblastoid	seeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30720600-30736600	Weak transcription	Gastric	stomach
2	chr6:30726800-30739000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr6:30728000-30737000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:30728200-30736600	Weak transcription	Aorta	Aorta
5	chr6:30731000-30738800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:30732000-30736600	Weak transcription	HSMM	muscle
7	chr6:30732000-30736800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:30732200-30736600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:30732200-30736800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:30732200-30737000	Weak transcription	Fetal Lung	lung
11	chr6:30732400-30736600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:30732400-30736600	Weak transcription	Colon Smooth Muscle	Colon
13	chr6:30732400-30736600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:30732400-30736800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:30732400-30736800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:30732400-30736800	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:30733200-30736600	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr6:30733400-30736800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:30733600-30736600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr6:30733800-30736600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:30734000-30736800	Enhancers	NH-A	brain
22	chr6:30734000-30737000	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr6:30734200-30737000	Enhancers	K562	blood
24	chr6:30734400-30736800	Enhancers	Primary T cells from cord blood	blood
25	chr6:30734400-30737000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr6:30734400-30738800	Enhancers	Fetal Thymus	thymus
27	chr6:30734600-30736600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr6:30734600-30736600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:30734600-30736600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr6:30734600-30736600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:30734600-30736600	Weak transcription	Pancreas	Pancrea
32	chr6:30734600-30736600	Weak transcription	Stomach Mucosa	stomach
33	chr6:30734600-30736800	Weak transcription	Fetal Heart	heart
34	chr6:30734600-30736800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr6:30734600-30737000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:30734800-30736600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr6:30734800-30736600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr6:30734800-30736600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr6:30734800-30738200	Enhancers	Primary T cells fromperipheralblood	blood
40	chr6:30734800-30747400	Weak transcription	Liver	Liver
41	chr6:30735000-30736600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:30735000-30737000	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr6:30735000-30738400	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr6:30735000-30738600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr6:30735000-30738800	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr6:30735200-30736600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr6:30735400-30736600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr6:30735400-30736600	Enhancers	Dnd41	blood
49	chr6:30735400-30736600	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr6:30735400-30736800	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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