Variant report

Variant	rs34727333
Chromosome Location	chr9:104299873-104299874
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr9:104298893-104299900	A549	lung:	n/a	chr9:104299413-104299422
2	REST	chr9:104298892-104299956	ECC-1	luminal epithelium:	n/a	chr9:104299413-104299422
3	REST	chr9:104298859-104299967	ECC-1	luminal epithelium:	n/a	chr9:104299413-104299422
4	REST	chr9:104298866-104299952	HL-60	blood:	n/a	chr9:104299413-104299422

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:104295154..104296821-chr9:104298164..104300262,2	MCF-7	breast:
2	chr9:104288484..104290134-chr9:104298816..104300608,2	K562	blood:

Variant related genes	Relation type
TMEM246	TF binding region
ENSG00000155827	Chromatin interaction
ENSG00000165152	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10115763	0.89[ASN][1000 genomes]
rs10125893	0.81[AMR][1000 genomes]
rs10989553	0.88[ASN][1000 genomes]
rs12342026	0.85[ASN][1000 genomes]
rs12342991	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12343288	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12347518	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13284984	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13290720	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13295809	0.84[ASN][1000 genomes]
rs16920473	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1885977	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1929496	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28533545	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34153995	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36004060	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3739722	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3824473	0.85[ASN][1000 genomes]
rs3903804	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4119332	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs45488691	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59770438	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7030238	0.89[ASN][1000 genomes]
rs7034754	0.99[ASN][1000 genomes]
rs9299345	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv893626	chr9:104172936-104324545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active 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	14 gene(s)	inside rSNPs	diseases
4	nsv1052492	chr9:104263419-104387782	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv893627	chr9:104268342-104334333	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104296600-104301800	Weak transcription	Spleen	Spleen
2	chr9:104296800-104300400	Enhancers	Fetal Heart	heart
3	chr9:104296800-104300600	Weak transcription	Esophagus	oesophagus
4	chr9:104296800-104302600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:104296800-104302600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:104296800-104302600	Weak transcription	Lung	lung
7	chr9:104296800-104302800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:104296800-104302800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:104296800-104305800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:104296800-104334200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr9:104296800-104337400	Weak transcription	Stomach Mucosa	stomach
12	chr9:104297000-104302000	Weak transcription	Fetal Stomach	stomach
13	chr9:104297000-104302600	Weak transcription	Colonic Mucosa	Colon
14	chr9:104297000-104302600	Weak transcription	NH-A	brain
15	chr9:104297000-104302800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr9:104297000-104302800	Weak transcription	HSMMtube	muscle
17	chr9:104297000-104309200	Weak transcription	HUVEC	blood vessel
18	chr9:104297000-104317600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr9:104297200-104302400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr9:104297200-104302600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr9:104297200-104302800	Weak transcription	Fetal Intestine Small	intestine
22	chr9:104297200-104309200	Weak transcription	K562	blood
23	chr9:104297400-104301400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
24	chr9:104297600-104300400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr9:104297600-104300400	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr9:104297600-104300800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
27	chr9:104297600-104300800	Strong transcription	Osteobl	bone
28	chr9:104297600-104301000	Genic enhancers	Brain Cingulate Gyrus	brain
29	chr9:104297600-104301000	Strong transcription	Fetal Muscle Trunk	muscle
30	chr9:104297600-104302800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr9:104297600-104304600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr9:104297600-104306000	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr9:104297600-104321200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr9:104297600-104330400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:104297600-104330400	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr9:104297800-104300400	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr9:104297800-104300800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr9:104297800-104300800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr9:104297800-104300800	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr9:104297800-104300800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr9:104297800-104300800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr9:104297800-104303800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr9:104297800-104303800	Strong transcription	Fetal Muscle Leg	muscle
44	chr9:104297800-104304800	Strong transcription	Fetal Lung	lung
45	chr9:104297800-104305800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr9:104297800-104311400	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr9:104297800-104317400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr9:104297800-104318400	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr9:104297800-104320400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr9:104297800-104320400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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