Variant report

Variant	rs13400128
Chromosome Location	chr2:10179657-10179658
allele	A/C
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:5)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:10177980..10179820-chr2:10584164..10586131,2	K562	blood:
2	chr2:9981748..9983787-chr2:10179341..10181254,2	K562	blood:
3	chr2:10108326..10110432-chr2:10178116..10179884,2	K562	blood:
4	chr2:10160149..10163716-chr2:10178459..10180847,3	MCF-7	breast:
5	chr2:9910191..9912681-chr2:10179231..10181515,2	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CYS1-1	chr2:10179219-10180790	ENSG00000260077.1
2	lnc-CYS1-1	chr2:10179240-10180791	NONHSAT069084
3	lnc-CYS1-1	chr2:10179240-10180791	NONHSAT069085

No data

Variant related genes	Relation type
ENSG00000260476	Chromatin interaction
ENSG00000243491	Chromatin interaction
ENSG00000115750	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10177872	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929632	1.00[ASN][1000 genomes]
rs11886661	1.00[ASN][1000 genomes]
rs3935840	1.00[ASN][1000 genomes]
rs4302193	1.00[ASN][1000 genomes]
rs4321336	1.00[ASN][1000 genomes]
rs4485541	1.00[ASN][1000 genomes]
rs4569449	1.00[ASN][1000 genomes]
rs4669527	1.00[ASN][1000 genomes]
rs6432058	1.00[ASN][1000 genomes]
rs6432060	1.00[ASN][1000 genomes]
rs72786623	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72786624	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7587317	1.00[ASN][1000 genomes]
rs7587529	1.00[ASN][1000 genomes]
rs7602408	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv997334	chr2:10080327-10189279	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv828297	chr2:10109299-10236332	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1007965	chr2:10154960-10276125	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription 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	80 gene(s)	inside rSNPs	diseases
6	nsv1014790	chr2:10156968-10274855	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
7	nsv999019	chr2:10157762-10273232	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
8	nsv873633	chr2:10175442-10266563	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
9	nsv828308	chr2:10175525-10200328	Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10170600-10182000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:10170800-10179800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:10170800-10182000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr2:10170800-10182000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:10170800-10182400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:10171000-10180000	Weak transcription	Fetal Brain Male	brain
7	chr2:10171400-10182000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr2:10171600-10182000	Weak transcription	Fetal Intestine Large	intestine
9	chr2:10173800-10182400	Weak transcription	Gastric	stomach
10	chr2:10175800-10180400	Enhancers	Brain Anterior Caudate	brain
11	chr2:10175800-10180600	Enhancers	Osteobl	bone
12	chr2:10175800-10181200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:10176000-10180400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:10176000-10181200	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr2:10176400-10182600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:10176600-10181800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:10176600-10182200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr2:10176600-10182400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr2:10176600-10182800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr2:10176800-10182000	Enhancers	Colon Smooth Muscle	Colon
21	chr2:10176800-10182200	Enhancers	Rectal Smooth Muscle	rectum
22	chr2:10176800-10182400	Enhancers	Adipose Nuclei	Adipose
23	chr2:10177000-10180200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:10177000-10182000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr2:10177000-10182200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr2:10177000-10182200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr2:10177000-10182200	Weak transcription	Fetal Brain Female	brain
28	chr2:10177200-10179800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr2:10177200-10181000	Weak transcription	Colonic Mucosa	Colon
30	chr2:10177200-10181200	Weak transcription	Stomach Mucosa	stomach
31	chr2:10177200-10182000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr2:10177200-10182200	Weak transcription	Fetal Lung	lung
33	chr2:10177200-10182400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr2:10177400-10180000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:10177600-10180800	Weak transcription	Fetal Heart	heart
36	chr2:10177600-10181400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:10177600-10182200	Weak transcription	Brain Angular Gyrus	brain
38	chr2:10177800-10179800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:10177800-10182400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:10178000-10179800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:10178000-10179800	Weak transcription	Pancreas	Pancrea
42	chr2:10178000-10179800	Enhancers	Stomach Smooth Muscle	stomach
43	chr2:10178000-10180800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:10178000-10182600	Weak transcription	A549	lung
45	chr2:10178200-10179800	Weak transcription	Ovary	ovary
46	chr2:10178200-10179800	Weak transcription	Right Atrium	heart
47	chr2:10178200-10179800	Weak transcription	NHEK	skin
48	chr2:10178200-10180000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:10178200-10181800	Weak transcription	Fetal Muscle Leg	muscle
50	chr2:10178200-10182000	Weak transcription	Primary monocytes fromperipheralblood	blood

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