Variant report

Variant	rs3132129
Chromosome Location	chr6:30027860-30027861
allele	C/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:4)
LncRNA
region (count:1)
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	chr6:30027738-30030222	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr6:30027606-30028052	H1-neurons	neurons:	n/a	n/a
3	REST	chr6:30027431-30030056	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr6:30027664-30028093	H1-neurons	neurons:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:30027015..30030813-chr6:30040823..30045193,4	K562	blood:
2	chr6:30001672..30004034-chr6:30026395..30027961,2	K562	blood:
3	chr6:30002424..30006428-chr6:30027567..30030890,5	MCF-7	breast:
4	chr6:30027269..30029063-chr6:30293187..30296080,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF39-4	chr6:30026145-30028756	ENSG00000204623

No data

Variant related genes	Relation type
ZNRD1-AS1	TF binding region
ZNRD1	TF binding region
ENSG00000231074	Chromatin interaction
ENSG00000204599	Chromatin interaction
ENSG00000204623	Chromatin interaction
ENSG00000204618	Chromatin interaction
ENSG00000270604	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs3121597	0.82[AMR][1000 genomes]
rs9261387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3132129	HCG22	cis	lymphoblastoid	seeQTL
rs3132129	HIST1H4L	cis	parietal	SCAN
rs3132129	HIST1H2BF	cis	parietal	SCAN
rs3132129	GRM4	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30014000-30028000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr6:30017400-30028400	Weak transcription	Lung	lung
3	chr6:30020400-30028200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:30025800-30028000	Weak transcription	Ovary	ovary
5	chr6:30027200-30028000	Enhancers	Liver	Liver
6	chr6:30027200-30028000	Enhancers	Fetal Heart	heart
7	chr6:30027400-30028200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:30027400-30028200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr6:30027400-30028200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:30027400-30028200	Flanking Active TSS	GM12878-XiMat	blood
11	chr6:30027600-30028000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr6:30027600-30028000	Enhancers	Primary B cells from cord blood	blood
13	chr6:30027600-30028000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr6:30027600-30028000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:30027600-30028000	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr6:30027600-30028000	Flanking Active TSS	Brain Anterior Caudate	brain
17	chr6:30027600-30028000	Enhancers	Brain Hippocampus Middle	brain
18	chr6:30027600-30028000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr6:30027600-30028000	Enhancers	Fetal Intestine Large	intestine
20	chr6:30027600-30028000	Flanking Active TSS	A549	lung
21	chr6:30027600-30028200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:30027600-30028200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:30027600-30028200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr6:30027600-30028200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr6:30027600-30028200	Enhancers	Fetal Brain Male	brain
26	chr6:30027600-30028200	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr6:30027600-30028200	Flanking Active TSS	K562	blood
28	chr6:30027600-30028200	Flanking Active TSS	NHEK	skin
29	chr6:30027600-30028400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:30027600-30028400	Flanking Active TSS	Dnd41	blood
31	chr6:30027600-30028600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr6:30027600-30028600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:30027600-30028800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:30027600-30028800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:30027600-30030200	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr6:30027600-30031000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:30027800-30028000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr6:30027800-30028000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
39	chr6:30027800-30028000	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr6:30027800-30028000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:30027800-30028000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:30027800-30028000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:30027800-30028000	Enhancers	Brain Substantia Nigra	brain
44	chr6:30027800-30028000	Flanking Active TSS	Fetal Kidney	kidney
45	chr6:30027800-30028000	Enhancers	Fetal Stomach	stomach
46	chr6:30027800-30028000	Enhancers	Fetal Thymus	thymus
47	chr6:30027800-30028000	Enhancers	Left Ventricle	heart
48	chr6:30027800-30028000	Flanking Active TSS	Psoas Muscle	Psoas
49	chr6:30027800-30028000	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr6:30027800-30028000	Flanking Active TSS	Right Ventricle	heart

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