Variant report

Variant	rs16846495
Chromosome Location	chr1:173839286-173839287
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr1:173839248-173839731	GM12878	blood:	n/a	chr1:173839528-173839541
2	ELF1	chr1:173839216-173839733	GM12878	blood:	n/a	chr1:173839528-173839541
3	POLR2A	chr1:173839277-173839802	GM12892	blood:	n/a	n/a
4	POLR2A	chr1:173839255-173839736	GM15510	blood:	n/a	n/a
5	ELF1	chr1:173839284-173839815	K562	blood:	n/a	chr1:173839528-173839541
6	JUN	chr1:173832403-173840952	K562	blood:	n/a	chr1:173837048-173837062 chr1:173840939-173840951 chr1:173837421-173837430 chr1:173837165-173837178 chr1:173837443-173837452 chr1:173833568-173833581 chr1:173837835-173837844 chr1:173840672-173840683 chr1:173837169-173837178
7	NFIC	chr1:173839113-173839757	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:173839257-173840049	GM12891	blood:	n/a	n/a
9	POLR2A	chr1:173839219-173839945	GM12892	blood:	n/a	n/a
10	POLR2A	chr1:173839251-173839838	GM12892	blood:	n/a	n/a
11	RUNX3	chr1:173839212-173839715	GM12878	blood:	n/a	n/a
12	RUNX3	chr1:173839197-173839776	GM12878	blood:	n/a	n/a
13	MXI1	chr1:173834502-173840026	SK-N-SH	brain:	n/a	n/a
14	TAF1	chr1:173839279-173839694	K562	blood:	n/a	n/a
15	FOXM1	chr1:173839277-173839760	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:173839228-173839871	GM12892	blood:	n/a	n/a
17	MAX	chr1:173839253-173839710	K562	blood:	n/a	n/a
18	PML	chr1:173839196-173839937	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:173839269-173839807	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:173839218-173839941	HUVEC	blood vessel:	n/a	n/a
21	MTA3	chr1:173839266-173839937	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:173839284-173839750	GM12891	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:173835651..173839404-chr1:173878959..173883807,5	K562	blood:
2	chr1:173837020..173839325-chr1:174127377..174129524,4	K562	blood:
3	chr1:173837529..173841751-chr1:173936779..173939459,3	K562	blood:
4	chr1:173834700..173840265-chr1:173989829..173994040,12	K562	blood:
5	chr1:173837862..173839508-chr1:173885268..173887307,2	MCF-7	breast:
6	chr1:173789792..173811494-chr1:173827886..173840273,103	K562	blood:
7	chr1:173833761..173839509-chr1:173990118..173994234,9	K562	blood:
8	chr1:173839047..173840684-chr1:173900730..173903519,2	K562	blood:
9	chr1:173835729..173840438-chr1:174127915..174131019,7	K562	blood:
10	chr1:173792463..173795572-chr1:173835250..173839446,8	MCF-7	breast:
11	chr1:173831314..173839948-chr1:173984831..173993131,14	MCF-7	breast:
12	chr1:173832421..173839801-chr1:173885332..173891780,9	MCF-7	breast:
13	chr1:173834428..173840700-chr1:173878764..173885322,14	MCF-7	breast:
14	chr1:173831906..173839548-chr1:173987374..173993282,15	MCF-7	breast:
15	chr1:173789473..173804179-chr1:173828884..173842109,95	K562	blood:
16	chr1:173833863..173839457-chr1:173910408..173918981,14	MCF-7	breast:

No data

Variant related genes	Relation type
GAS5	TF binding region
SNORD78	TF binding region
ENSG00000252231	Chromatin interaction
ENSG00000227373	Chromatin interaction
ENSG00000200755	Chromatin interaction
ENSG00000117601	Chromatin interaction
ENSG00000117593	Chromatin interaction
ENSG00000135870	Chromatin interaction
ENSG00000120334	Chromatin interaction
ENSG00000224977	Chromatin interaction
ENSG00000236535	Chromatin interaction
ENSG00000152061	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10082342	1.00[CHD][hapmap]
rs12726669	1.00[AMR][1000 genomes]
rs2180327	1.00[CHD][hapmap]
rs35054401	1.00[AMR][1000 genomes]
rs7550107	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173838000-173840800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:173838200-173839400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:173838200-173839400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:173838200-173839400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:173838200-173839400	Weak transcription	Left Ventricle	heart
6	chr1:173838200-173839400	Weak transcription	Pancreas	Pancrea
7	chr1:173838200-173839400	Weak transcription	Spleen	Spleen
8	chr1:173838200-173839800	Weak transcription	Lung	lung
9	chr1:173838200-173846600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:173838200-173854200	Weak transcription	Gastric	stomach
11	chr1:173838200-173866000	Weak transcription	Small Intestine	intestine
12	chr1:173838400-173839400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:173838400-173839400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr1:173838400-173839400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:173838400-173839400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr1:173838400-173839400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:173838400-173839600	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr1:173838400-173839600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:173838400-173839600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:173838400-173839600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:173838400-173839600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr1:173838400-173839600	Weak transcription	Psoas Muscle	Psoas
23	chr1:173838400-173839600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:173838400-173839800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr1:173838400-173839800	Enhancers	Brain Anterior Caudate	brain
26	chr1:173838400-173839800	Weak transcription	Fetal Brain Male	brain
27	chr1:173838400-173839800	Flanking Active TSS	GM12878-XiMat	blood
28	chr1:173838400-173841000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr1:173838400-173844600	Weak transcription	Ovary	ovary
30	chr1:173838400-173844800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:173838400-173854200	Weak transcription	Esophagus	oesophagus
32	chr1:173838400-173854800	Weak transcription	Aorta	Aorta
33	chr1:173838400-173854800	Weak transcription	Right Ventricle	heart
34	chr1:173838400-173860200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:173838600-173839400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:173838600-173839400	Enhancers	Primary B cells from cord blood	blood
37	chr1:173838600-173839400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:173838600-173839400	Enhancers	Adipose Nuclei	Adipose
39	chr1:173838600-173839400	Enhancers	Brain Cingulate Gyrus	brain
40	chr1:173838600-173839400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr1:173838600-173839400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:173838600-173839400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:173838600-173839400	Weak transcription	Thymus	Thymus
44	chr1:173838600-173839400	Weak transcription	HSMMtube	muscle
45	chr1:173838600-173839600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:173838600-173839600	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr1:173838600-173839600	Weak transcription	Osteobl	bone
48	chr1:173838600-173839800	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr1:173838600-173841000	Enhancers	Stomach Mucosa	stomach
50	chr1:173838600-173854800	Weak transcription	Rectal Smooth Muscle	rectum

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