Variant report

Variant	rs1856161
Chromosome Location	chr1:209959168-209959169
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr1:209958985-209960088	PBDE	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:209955222..209959394-chr1:210545816..210547914,4	K562	blood:
2	chr1:209955520..209962214-chr1:209976009..209982555,8	K562	blood:
3	chr1:209940429..209942619-chr1:209957623..209959222,2	MCF-7	breast:
4	chr1:209957348..209959526-chr1:209965730..209967837,2	K562	blood:
5	chr1:209950429..209953463-chr1:209956092..209959569,7	K562	blood:
6	chr1:209957965..209959806-chr1:209959959..209962744,2	K562	blood:
7	chr1:209954505..209956563-chr1:209958183..209960148,2	K562	blood:
8	chr1:209957266..209960368-chr1:209964452..209967778,3	MCF-7	breast:
9	chr1:209955602..209959674-chr1:209962858..209967873,6	MCF-7	breast:
10	chr1:209956289..209959543-chr1:209978892..209981541,4	K562	blood:
11	chr1:209958606..209961246-chr1:209973550..209976119,2	MCF-7	breast:

No data

Variant related genes	Relation type
C1orf74	TF binding region
ENSG00000200972	Chromatin interaction
ENSG00000117595	Chromatin interaction
ENSG00000232222	Chromatin interaction
ENSG00000009790	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10489343	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10779514	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10779515	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10863789	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10863790	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1109430	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11119345	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11119346	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119347	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119348	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119360	1.00[AFR][1000 genomes]
rs11585733	1.00[AFR][1000 genomes]
rs11589335	1.00[AFR][1000 genomes]
rs12058100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12062600	1.00[AFR][1000 genomes]
rs12063989	1.00[AFR][1000 genomes]
rs12064085	1.00[AFR][1000 genomes]
rs12064211	1.00[AFR][1000 genomes]
rs12064398	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12066340	1.00[AFR][1000 genomes]
rs12069187	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12075674	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12080691	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12081405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12083685	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12405750	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12561766	1.00[AFR][1000 genomes]
rs12563527	1.00[AFR][1000 genomes]
rs12566152	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13306422	1.00[AFR][1000 genomes]
rs17015217	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17015255	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17015268	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17388240	1.00[AFR][1000 genomes]
rs1883332	1.00[AFR][1000 genomes]
rs2038053	1.00[AFR][1000 genomes]
rs2069068	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2076149	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2076151	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2142860	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2235370	0.94[AMR][1000 genomes]
rs2235371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2235377	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2272866	1.00[AFR][1000 genomes]
rs2282740	1.00[AFR][1000 genomes]
rs2294406	0.84[AMR][1000 genomes]
rs3753517	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41274836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4140636	0.80[EUR][1000 genomes]
rs4329516	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4844491	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4844494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4844496	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4844893	1.00[AFR][1000 genomes]
rs4844894	1.00[AFR][1000 genomes]
rs4844908	1.00[AFR][1000 genomes]
rs57283682	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv4343	chr1:209929932-209974877	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1067914	chr1:209955818-209972979	Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
7	nsv945273	chr1:209958252-209960036	Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209957800-209978600	Weak transcription	Spleen	Spleen
2	chr1:209958000-209960600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:209958000-209961000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:209958000-209961400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:209958000-209971600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:209958200-209959200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr1:209958200-209962600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:209958200-209963800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:209958400-209959400	Genic enhancers	HMEC	breast
10	chr1:209958400-209960200	Weak transcription	Right Atrium	heart
11	chr1:209958400-209960600	Enhancers	Liver	Liver
12	chr1:209958400-209960800	Enhancers	Left Ventricle	heart
13	chr1:209958400-209961800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:209958400-209962200	Weak transcription	Esophagus	oesophagus
15	chr1:209958400-209962200	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr1:209958400-209962400	Enhancers	Stomach Mucosa	stomach
17	chr1:209958400-209962800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:209958400-209968600	Weak transcription	Lung	lung
19	chr1:209958400-209971800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:209958400-209974000	Weak transcription	Aorta	Aorta
21	chr1:209958400-209978600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:209958600-209959400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:209958600-209959600	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:209958600-209959600	Strong transcription	Fetal Intestine Small	intestine
25	chr1:209958600-209959800	Weak transcription	Adipose Nuclei	Adipose
26	chr1:209958600-209959800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:209958600-209959800	Strong transcription	Fetal Intestine Large	intestine
28	chr1:209958600-209959800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr1:209958600-209960000	Genic enhancers	Duodenum Mucosa	Duodenum
30	chr1:209958600-209960200	Weak transcription	Gastric	stomach
31	chr1:209958600-209960200	Weak transcription	Pancreas	Pancrea
32	chr1:209958600-209960400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:209958600-209960400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:209958600-209960400	Weak transcription	Colonic Mucosa	Colon
35	chr1:209958600-209960400	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr1:209958600-209960400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr1:209958600-209960600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:209958600-209960800	Weak transcription	Placenta	Placenta
39	chr1:209958600-209961200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:209958600-209961400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:209958600-209961400	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr1:209958600-209962400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr1:209958600-209963600	Weak transcription	HUVEC	blood vessel
44	chr1:209958600-209966200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr1:209958600-209966600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr1:209958600-209967000	Genic enhancers	NHEK	skin
47	chr1:209958600-209971200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:209958600-209972000	Weak transcription	Fetal Kidney	kidney
49	chr1:209958600-209978800	Weak transcription	Right Ventricle	heart
50	chr1:209958800-209959200	Weak transcription	Small Intestine	intestine

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