Variant report

Variant	rs1001304
Chromosome Location	chr1:212732686-212732687
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:15)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212730682..212733368-chr1:212780704..212783808,5	MCF-7	breast:
2	chr1:212730770..212733133-chr1:212778739..212783577,4	MCF-7	breast:
3	chr1:212688702..212690352-chr1:212731451..212733749,2	K562	blood:
4	chr1:212729491..212744666-chr1:212778733..212791648,68	K562	blood:
5	chr1:212731186..212732760-chr1:212816538..212818600,2	K562	blood:
6	chr1:212731550..212733593-chr1:212839647..212842156,2	K562	blood:
7	chr1:212650902..212653623-chr1:212731690..212733930,2	K562	blood:
8	chr1:212731680..212733732-chr1:212810239..212812823,2	K562	blood:
9	chr1:212729172..212744062-chr1:212776412..212791648,77	K562	blood:
10	chr1:211903185..211904905-chr1:212731806..212733794,2	K562	blood:
11	chr1:212676521..212678567-chr1:212731276..212732925,2	K562	blood:
12	chr1:212702412..212705298-chr1:212732068..212734031,2	K562	blood:
13	chr1:212717692..212719261-chr1:212731770..212733992,2	K562	blood:
14	chr1:212717692..212719573-chr1:212732031..212733992,2	K562	blood:
15	chr1:212674417..212676345-chr1:212732607..212734870,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATF3-1	chr1:212732498-212733380	XLOC_000555
2	lnc-ATF3-1	chr1:212731175-212733073	ENSG00000260805.1

No data

Variant related genes	Relation type
ENSG00000162772	Chromatin interaction
ENSG00000264590	Chromatin interaction
ENSG00000228067	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1021378	0.87[JPT][hapmap]
rs11802726	0.90[YRI][hapmap]
rs11805307	0.85[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs1195472	0.91[JPT][hapmap]
rs1388032	0.90[YRI][hapmap]
rs3125289	0.86[JPT][hapmap]
rs6659881	0.87[JPT][hapmap]
rs791851	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
5	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
6	nsv428588	chr1:212705588-212862875	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1001304	C1orf74	cis	parietal	SCAN
rs1001304	HHAT	cis	cerebellum	SCAN
rs1001304	FAM71A	cis	cerebellum	SCAN
rs1001304	FAIM3	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212731200-212732800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr1:212731200-212732800	Active TSS	Fetal Brain Female	brain
3	chr1:212731400-212732800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:212731400-212732800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:212731600-212732800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:212731600-212732800	Active TSS	Ovary	ovary
7	chr1:212731600-212732800	Flanking Active TSS	HMEC	breast
8	chr1:212731800-212732800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
9	chr1:212731800-212732800	Active TSS	Liver	Liver
10	chr1:212731800-212732800	Bivalent/Poised TSS	Fetal Stomach	stomach
11	chr1:212731800-212733000	Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr1:212731800-212733000	Flanking Active TSS	Dnd41	blood
13	chr1:212732200-212733000	Flanking Bivalent TSS/Enh	HepG2	liver
14	chr1:212732400-212732800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:212732400-212732800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:212732400-212732800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr1:212732400-212732800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:212732400-212732800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
19	chr1:212732400-212732800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr1:212732400-212732800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:212732400-212732800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr1:212732400-212732800	Flanking Active TSS	Primary B cells from peripheral blood	blood
23	chr1:212732400-212732800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr1:212732400-212732800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:212732400-212732800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr1:212732400-212732800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:212732400-212732800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:212732400-212732800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:212732400-212732800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:212732400-212732800	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr1:212732400-212732800	Flanking Active TSS	Brain Angular Gyrus	brain
32	chr1:212732400-212732800	Flanking Active TSS	Colon Smooth Muscle	Colon
33	chr1:212732400-212732800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr1:212732400-212732800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr1:212732400-212732800	Flanking Active TSS	Fetal Lung	lung
36	chr1:212732400-212732800	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr1:212732400-212732800	Flanking Active TSS	Fetal Thymus	thymus
38	chr1:212732400-212732800	Enhancers	Left Ventricle	heart
39	chr1:212732400-212732800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr1:212732400-212732800	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr1:212732400-212732800	Enhancers	Small Intestine	intestine
42	chr1:212732400-212732800	Flanking Active TSS	Stomach Mucosa	stomach
43	chr1:212732400-212732800	Flanking Active TSS	Hela-S3	cervix
44	chr1:212732400-212732800	Flanking Active TSS	HSMMtube	muscle
45	chr1:212732400-212732800	Flanking Active TSS	HUVEC	blood vessel
46	chr1:212732400-212732800	Flanking Active TSS	K562	blood
47	chr1:212732400-212732800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr1:212732400-212732800	Enhancers	NH-A	brain
49	chr1:212732400-212732800	Flanking Active TSS	NHEK	skin
50	chr1:212732400-212732800	Flanking Active TSS	Osteobl	bone

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