Variant report

Variant	rs6427268
Chromosome Location	chr1:153720690-153720691
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:153720660-153720810	GM12872	blood:	n/a	n/a
2	CTCF	chr1:153720620-153720770	WERI-Rb-1	eye:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:153718689..153722494-chr1:153754565..153757255,3	MCF-7	breast:
2	chr1:153720153..153722132-chr1:153938351..153940941,2	K562	blood:
3	chr1:153649696..153652136-chr1:153718198..153722635,6	MCF-7	breast:
4	chr1:153716182..153721431-chr1:153722376..153725586,6	K562	blood:
5	chr1:153641918..153644104-chr1:153718831..153722451,3	MCF-7	breast:
6	chr1:153601574..153604537-chr1:153718761..153721275,2	K562	blood:
7	chr1:153619135..153622133-chr1:153720546..153722065,2	K562	blood:
8	chr1:153716864..153718651-chr1:153718917..153721137,2	K562	blood:
9	chr1:153719991..153722380-chr1:153747538..153749558,2	K562	blood:
10	chr1:153604435..153608010-chr1:153720589..153722961,3	MCF-7	breast:
11	chr1:153707078..153709228-chr1:153718414..153722643,3	MCF-7	breast:
12	chr1:153601040..153604537-chr1:153718761..153722093,3	K562	blood:
13	chr1:153651041..153652767-chr1:153718619..153721347,2	MCF-7	breast:
14	chr1:153588561..153590573-chr1:153720516..153722822,2	K562	blood:
15	chr1:153650233..153650842-chr1:153719963..153721239,3	MCF-7	breast:
16	chr1:153698814..153704322-chr1:153719587..153724035,6	MCF-7	breast:

No data

Variant related genes	Relation type
INTS3	TF binding region
ENSG00000160679	Chromatin interaction
ENSG00000233222	Chromatin interaction
ENSG00000189334	Chromatin interaction
ENSG00000273026	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000243613	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000199565	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000169418	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000143624	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12041194	0.82[ASN][1000 genomes]
rs6427183	0.91[EUR][1000 genomes]
rs6677628	0.93[EUR][1000 genomes]
rs7545253	0.83[EUR][1000 genomes]
rs7554642	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9426891	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9426901	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9426902	0.88[ASN][1000 genomes]
rs9427217	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830411	chr1:153613393-153725007	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1067771	chr1:153613593-153724866	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Enhancers Active TSS 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 miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv530052	chr1:153613593-153724866	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv1005818	chr1:153613597-153724980	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv535173	chr1:153613597-153724980	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv1007835	chr1:153613597-153729959	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer 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	48 gene(s)	inside rSNPs	diseases
7	nsv535174	chr1:153613597-153729959	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
9	nsv464028	chr1:153622220-153723037	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv547929	chr1:153622220-153723037	Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers 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	286 gene(s)	inside rSNPs	diseases
12	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
13	nsv1001312	chr1:153622834-153724867	Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv535176	chr1:153622834-153724867	Active TSS Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
16	nsv464039	chr1:153708906-153801098	Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
17	nsv547941	chr1:153708906-153801098	Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer 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	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6427268	S100A2	cis	cerebellum	SCAN
rs6427268	S100A9	cis	parietal	SCAN
rs6427268	S100A13	cis	parietal	SCAN
rs6427268	KPRP	cis	parietal	SCAN
rs6427268	S100A10	cis	cerebellum	SCAN
rs6427268	S100A16	cis	cerebellum	SCAN
rs6427268	LCE1B	cis	parietal	SCAN
rs6427268	SLC27A3	cis	cerebellum	SCAN
rs6427268	S100A10	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153707200-153730400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:153707600-153722200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:153711400-153735600	Strong transcription	Fetal Muscle Leg	muscle
4	chr1:153711600-153721400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:153712600-153721800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:153712600-153721800	Strong transcription	Brain Anterior Caudate	brain
7	chr1:153712600-153722400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:153712600-153741400	Strong transcription	Placenta	Placenta
9	chr1:153712800-153721800	Strong transcription	Brain Inferior Temporal Lobe	brain
10	chr1:153712800-153721800	Strong transcription	Colon Smooth Muscle	Colon
11	chr1:153712800-153725600	Strong transcription	Fetal Lung	lung
12	chr1:153712800-153737800	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr1:153712800-153737800	Strong transcription	Placenta Amnion	Placenta Amnion
14	chr1:153712800-153738000	Strong transcription	Fetal Brain Female	brain
15	chr1:153712800-153738200	Strong transcription	Thymus	Thymus
16	chr1:153712800-153742800	Strong transcription	Fetal Muscle Trunk	muscle
17	chr1:153712800-153743200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:153712800-153744800	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr1:153712800-153746400	Strong transcription	Brain Germinal Matrix	brain
20	chr1:153712800-153751800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:153713000-153721400	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:153713000-153721400	Strong transcription	Brain Cingulate Gyrus	brain
23	chr1:153713000-153721400	Strong transcription	Hela-S3	cervix
24	chr1:153713000-153721800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:153713000-153721800	Strong transcription	Adipose Nuclei	Adipose
26	chr1:153713000-153721800	Strong transcription	Brain Hippocampus Middle	brain
27	chr1:153713000-153722000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:153713000-153725600	Strong transcription	Primary hematopoietic stem cells	blood
29	chr1:153713000-153728600	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr1:153713000-153734800	Strong transcription	Spleen	Spleen
31	chr1:153713000-153735200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:153713000-153738200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:153713000-153738600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr1:153713000-153745400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr1:153713000-153745400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:153713000-153746400	Strong transcription	Primary T cells from cord blood	blood
37	chr1:153713000-153747000	Strong transcription	Dnd41	blood
38	chr1:153713200-153721400	Strong transcription	HUVEC	blood vessel
39	chr1:153713800-153721800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:153714000-153746800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:153715200-153738000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:153715400-153723000	Weak transcription	Right Atrium	heart
43	chr1:153715400-153724600	Strong transcription	NH-A	brain
44	chr1:153715400-153724800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:153715400-153745600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:153715600-153721400	Strong transcription	Gastric	stomach
47	chr1:153715600-153721800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:153715600-153725600	Strong transcription	NHEK	skin
49	chr1:153715600-153727600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:153715600-153745600	Strong transcription	Fetal Thymus	thymus

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