Variant report

Variant	rs35502594
Chromosome Location	chr10:99097398-99097399
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:39)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:39 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP4	chr10:99096780-99097455	H1-hESC	embryonic stem cell:	n/a	n/a
2	ESR1	chr10:99096637-99097516	T-47D	breast:	n/a	n/a
3	HDAC2	chr10:99096661-99097553	H1-hESC	embryonic stem cell:	n/a	n/a
4	ESR1	chr10:99096775-99097473	T-47D	breast:	n/a	n/a
5	HDAC2	chr10:99097126-99097569	MCF-7	breast:	n/a	n/a
6	NFIC	chr10:99096673-99097573	ECC-1	luminal epithelium:	n/a	n/a
7	CTBP2	chr10:99096752-99097457	H1-hESC	embryonic stem cell:	n/a	n/a
8	TAF1	chr10:99096744-99097455	H1-hESC	embryonic stem cell:	n/a	n/a
9	GATA3	chr10:99096831-99097495	MCF-7	breast:	n/a	n/a
10	POU5F1	chr10:99096680-99097398	H1-hESC	embryonic stem cell:	n/a	chr10:99097129-99097143 chr10:99097129-99097143 chr10:99097129-99097143
11	NR2F2	chr10:99096681-99097549	MCF-7	breast:	n/a	n/a
12	SIN3AK20	chr10:99096590-99097656	MCF-7	breast:	n/a	n/a
13	TCF7L2	chr10:99096703-99097411	MCF-7	breast:	n/a	n/a
14	SP1	chr10:99096604-99097447	H1-hESC	embryonic stem cell:	n/a	chr10:99096811-99096821 chr10:99096811-99096821 chr10:99096810-99096822
15	HDAC2	chr10:99096675-99097575	MCF-7	breast:	n/a	n/a
16	ATF2	chr10:99096638-99097540	H1-hESC	embryonic stem cell:	n/a	n/a
17	KAP1	chr10:99096678-99097580	U2OS	brain:	n/a	n/a
18	EP300	chr10:99097136-99097554	MCF-7	breast:	n/a	n/a
19	KAP1	chr10:99096711-99097532	HEK293	kidney:	n/a	n/a
20	TBP	chr10:99096606-99097468	H1-hESC	embryonic stem cell:	n/a	n/a
21	ZNF217	chr10:99096734-99097514	MCF-7	breast:	n/a	n/a
22	SP1	chr10:99096609-99097432	H1-hESC	embryonic stem cell:	n/a	chr10:99096811-99096821 chr10:99096811-99096821 chr10:99096810-99096822
23	YY1	chr10:99096982-99097534	H1-hESC	embryonic stem cell:	n/a	n/a
24	ESR1	chr10:99096733-99097501	T-47D	breast:	n/a	n/a
25	FOXA1	chr10:99096674-99097516	T-47D	breast:	n/a	n/a
26	EP300	chr10:99096708-99097533	T-47D	breast:	n/a	n/a
27	GATA3	chr10:99096626-99097453	T-47D	breast:	n/a	n/a
28	TCF7L2	chr10:99096755-99097449	PANC-1	pancreas:	n/a	n/a
29	HDAC2	chr10:99096809-99097565	H1-hESC	embryonic stem cell:	n/a	n/a
30	EP300	chr10:99096713-99097586	T-47D	breast:	n/a	n/a
31	NFIC	chr10:99096569-99097617	ECC-1	luminal epithelium:	n/a	n/a
32	ESR1	chr10:99096657-99097501	T-47D	breast:	n/a	n/a
33	FOXA1	chr10:99096752-99097439	T-47D	breast:	n/a	n/a
34	BACH1	chr10:99096611-99097505	H1-hESC	embryonic stem cell:	n/a	n/a
35	GATA3	chr10:99096615-99097617	MCF-7	breast:	n/a	n/a
36	JUND	chr10:99096745-99097502	H1-hESC	embryonic stem cell:	n/a	chr10:99096768-99096776
37	CREB1	chr10:99096657-99097464	H1-hESC	embryonic stem cell:	n/a	n/a
38	ESR1	chr10:99096669-99097487	T-47D	breast:	n/a	n/a
39	GATA3	chr10:99096677-99097409	T-47D	breast:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:99051072..99053903-chr10:99096331..99098905,2	MCF-7	breast:
2	chr10:99095023..99098677-chr10:99109833..99114591,4	MCF-7	breast:
3	chr10:99095422..99098240-chr10:99107284..99109589,2	MCF-7	breast:
4	chr10:99095891..99098123-chr10:99100617..99102682,2	K562	blood:

No data

Variant related genes	Relation type
FRAT2	TF binding region
ENSG00000269891	Chromatin interaction
ENSG00000213390	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs17557994	0.82[EUR][1000 genomes]
rs2297990	0.82[EUR][1000 genomes]
rs28362478	0.82[EUR][1000 genomes]
rs28987110	0.80[EUR][1000 genomes]
rs41300215	0.82[EUR][1000 genomes]
rs41300217	0.82[EUR][1000 genomes]
rs41303833	0.82[EUR][1000 genomes]
rs4917767	0.82[EUR][1000 genomes]
rs4917769	0.82[EUR][1000 genomes]
rs4919095	0.84[EUR][1000 genomes]
rs59058784	0.82[EUR][1000 genomes]
rs60305070	0.84[EUR][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	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1045553	chr10:98944397-99122203	Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv540750	chr10:98944397-99122203	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv831952	chr10:98998344-99145924	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv895914	chr10:99006083-99131676	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv825533	chr10:99070570-99115599	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv825534	chr10:99081505-99115599	Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription 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	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99095200-99097400	Enhancers	Stomach Mucosa	stomach
2	chr10:99095200-99097600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr10:99095200-99097600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr10:99095200-99109400	Weak transcription	HSMMtube	muscle
5	chr10:99095200-99115200	Weak transcription	Gastric	stomach
6	chr10:99095400-99097400	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr10:99095400-99097400	Enhancers	A549	lung
8	chr10:99095400-99097600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr10:99095400-99097600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr10:99095400-99098000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr10:99095400-99098000	Enhancers	Placenta	Placenta
12	chr10:99095400-99098200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr10:99095400-99098600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr10:99095400-99109400	Weak transcription	Liver	Liver
15	chr10:99095400-99115600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr10:99095400-99115600	Weak transcription	Left Ventricle	heart
17	chr10:99095400-99115600	Weak transcription	Right Ventricle	heart
18	chr10:99095600-99098200	Enhancers	Brain Angular Gyrus	brain
19	chr10:99095600-99101800	Weak transcription	Pancreas	Pancrea
20	chr10:99095800-99097600	Enhancers	HMEC	breast
21	chr10:99095800-99098400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr10:99095800-99098400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr10:99095800-99098400	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr10:99096000-99097400	Flanking Active TSS	NHEK	skin
25	chr10:99096000-99097600	Enhancers	Placenta Amnion	Placenta Amnion
26	chr10:99096000-99098400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr10:99096200-99097800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr10:99096400-99097400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr10:99096400-99097400	Enhancers	Fetal Intestine Small	intestine
30	chr10:99096400-99097600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr10:99096400-99098200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr10:99096400-99098200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr10:99096400-99098400	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr10:99096600-99097400	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr10:99096600-99097400	Enhancers	Psoas Muscle	Psoas
36	chr10:99096600-99097400	Bivalent Enhancer	HSMM	muscle
37	chr10:99096600-99097400	Bivalent Enhancer	NHDF-Ad	bronchial
38	chr10:99096600-99098200	Enhancers	Brain Cingulate Gyrus	brain
39	chr10:99096600-99098200	Bivalent Enhancer	Fetal Brain Male	brain
40	chr10:99096600-99098400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr10:99096800-99097400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr10:99096800-99097400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr10:99096800-99097400	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr10:99096800-99097400	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr10:99096800-99097400	Enhancers	Brain Hippocampus Middle	brain
46	chr10:99096800-99097400	Bivalent Enhancer	Fetal Muscle Leg	muscle
47	chr10:99096800-99097400	Enhancers	Right Atrium	heart
48	chr10:99096800-99097400	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr10:99096800-99097400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr10:99096800-99097600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

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