Variant report

Variant	rs17022063
Chromosome Location	chr2:99526289-99526290
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	MYC	chr2:99526189-99526389	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr2:99525808-99526433	MCF-7	breast:	n/a	n/a
3	RCOR1	chr2:99525979-99526361	HepG2	liver:	n/a	n/a
4	NFIC	chr2:99525830-99526460	ECC-1	luminal epithelium:	n/a	n/a
5	RCOR1	chr2:99525172-99526427	IMR90	lung:	n/a	n/a
6	PBX3	chr2:99525417-99526425	SK-N-SH	brain:	n/a	n/a
7	SPI1	chr2:99525848-99526727	HL-60	blood:	n/a	chr2:99526642-99526655 chr2:99526644-99526653
8	TCF12	chr2:99525748-99526580	ECC-1	luminal epithelium:	n/a	chr2:99526134-99526141 chr2:99526133-99526143 chr2:99526130-99526140 chr2:99526555-99526565
9	GATA3	chr2:99525491-99526620	MCF-7	breast:	n/a	chr2:99525900-99525921 chr2:99525907-99525914 chr2:99525905-99525914 chr2:99525902-99525918 chr2:99525906-99525914 chr2:99526409-99526419
10	KAP1	chr2:99525456-99526332	U2OS	brain:	n/a	chr2:99525647-99525655
11	MAX	chr2:99525757-99526535	ECC-1	luminal epithelium:	n/a	n/a
12	NFIC	chr2:99525682-99526456	SK-N-SH	brain:	n/a	n/a
13	KAP1	chr2:99524638-99526493	HEK293	kidney:	n/a	chr2:99525647-99525655
14	TCF12	chr2:99525641-99526615	MCF-7	breast:	n/a	chr2:99526134-99526141 chr2:99526133-99526143 chr2:99526130-99526140 chr2:99526555-99526565
15	MAX	chr2:99525870-99526428	H1-hESC	embryonic stem cell:	n/a	n/a
16	EP300	chr2:99525816-99526524	ECC-1	luminal epithelium:	n/a	chr2:99526408-99526417
17	CHD2	chr2:99526016-99526315	H1-hESC	embryonic stem cell:	n/a	n/a
18	EP300	chr2:99525757-99526350	T-47D	breast:	n/a	n/a
19	NFIC	chr2:99525625-99526620	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr2:99525887-99526635	HUVEC	blood vessel:	n/a	n/a
21	E2F6	chr2:99525903-99526410	H1-hESC	embryonic stem cell:	n/a	n/a
22	FOXA1	chr2:99525846-99526411	T-47D	breast:	n/a	n/a
23	NR2F2	chr2:99525686-99526493	MCF-7	breast:	n/a	n/a
24	MAX	chr2:99525752-99526374	SK-N-SH	brain:	n/a	n/a
25	TCF12	chr2:99525485-99526582	SK-N-SH	brain:	n/a	chr2:99526134-99526141 chr2:99526133-99526143 chr2:99526130-99526140 chr2:99526555-99526565
26	MYC	chr2:99525945-99526319	MCF-7	breast:	n/a	n/a
27	POLR2A	chr2:99525843-99526604	HUVEC	blood vessel:	n/a	n/a
28	TEAD4	chr2:99525762-99526413	SK-N-SH	brain:	n/a	n/a
29	GATA3	chr2:99525440-99526529	SK-N-SH	brain:	n/a	chr2:99525900-99525921 chr2:99525907-99525914 chr2:99525905-99525914 chr2:99525902-99525918 chr2:99525906-99525914 chr2:99526409-99526419
30	HDAC2	chr2:99525764-99526352	MCF-7	breast:	n/a	chr2:99526210-99526224 chr2:99525906-99525915
31	GATA3	chr2:99525509-99526428	MCF-7	breast:	n/a	chr2:99525900-99525921 chr2:99525907-99525914 chr2:99525905-99525914 chr2:99525902-99525918 chr2:99525906-99525914 chr2:99526409-99526419
32	MAX	chr2:99525867-99526484	H1-hESC	embryonic stem cell:	n/a	n/a
33	MXI1	chr2:99525897-99526314	HepG2	liver:	n/a	chr2:99526196-99526205
34	USF1	chr2:99525913-99526329	SK-N-SH	brain:	n/a	n/a
35	FOXA1	chr2:99525878-99526338	HepG2	liver:	n/a	n/a
36	GATA3	chr2:99525537-99526404	T-47D	breast:	n/a	chr2:99525900-99525921 chr2:99525907-99525914 chr2:99525905-99525914 chr2:99525902-99525918 chr2:99525906-99525914
37	RXRA	chr2:99525722-99526406	SK-N-SH	brain:	n/a	n/a
38	MAX	chr2:99525388-99526602	NB4	blood:	n/a	n/a
39	YY1	chr2:99525978-99526648	H1-hESC	embryonic stem cell:	n/a	n/a
40	MYBL2	chr2:99525740-99526349	HepG2	liver:	n/a	n/a
41	PBX3	chr2:99525354-99526506	SK-N-SH	brain:	n/a	n/a
42	MAX	chr2:99525781-99526383	SK-N-SH	brain:	n/a	n/a
43	TCF12	chr2:99525241-99526670	SK-N-SH	brain:	n/a	chr2:99526134-99526141 chr2:99526133-99526143 chr2:99526130-99526140 chr2:99526555-99526565
44	FOS	chr2:99525384-99526669	HUVEC	blood vessel:	n/a	n/a
45	ELF1	chr2:99525796-99526449	MCF-7	breast:	n/a	n/a
46	GATA3	chr2:99525678-99526402	T-47D	breast:	n/a	chr2:99525900-99525921 chr2:99525907-99525914 chr2:99525905-99525914 chr2:99525902-99525918 chr2:99525906-99525914
47	TCF12	chr2:99525732-99526523	ECC-1	luminal epithelium:	n/a	chr2:99526134-99526141 chr2:99526133-99526143 chr2:99526130-99526140
48	MAX	chr2:99525883-99526471	ECC-1	luminal epithelium:	n/a	n/a
49	E2F6	chr2:99525878-99526631	H1-hESC	embryonic stem cell:	n/a	n/a
50	GATA3	chr2:99525543-99526524	SK-N-SH	brain:	n/a	chr2:99525900-99525921 chr2:99525907-99525914 chr2:99525905-99525914 chr2:99525902-99525918 chr2:99525906-99525914 chr2:99526409-99526419

No.	Distal block	Cell Line	Cell type
1	chr2:99514144..99517054-chr2:99525112..99527785,2	MCF-7	breast:
2	chr2:99484412..99487919-chr2:99523957..99528531,6	MCF-7	breast:
3	chr2:99525536..99528520-chr2:99541090..99543085,2	MCF-7	breast:

Variant related genes	Relation type
KIAA1211L	TF binding region
ENSG00000196872	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12611969	1.00[YRI][hapmap]
rs12616060	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs12623171	1.00[YRI][hapmap]
rs868921	1.00[YRI][hapmap];0.85[AFR][1000 genomes]

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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582518	chr2:99498774-99546355	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv874697	chr2:99520608-99558970	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99520800-99528600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:99523800-99526600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr2:99523800-99526800	Enhancers	Esophagus	oesophagus
4	chr2:99523800-99530000	Enhancers	Fetal Muscle Leg	muscle
5	chr2:99524400-99526600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:99524400-99528400	Enhancers	HMEC	breast
7	chr2:99524400-99534400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:99524600-99526600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:99524600-99526600	Enhancers	Stomach Mucosa	stomach
10	chr2:99524600-99526800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:99524600-99526800	Enhancers	NHEK	skin
12	chr2:99524600-99532400	Enhancers	Pancreas	Pancrea
13	chr2:99524800-99526400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:99524800-99526400	Enhancers	Placenta	Placenta
15	chr2:99524800-99526400	Enhancers	NHLF	lung
16	chr2:99524800-99526600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr2:99524800-99526600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:99524800-99526600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr2:99524800-99526600	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr2:99524800-99526600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:99524800-99526600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:99524800-99526600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:99524800-99526600	Enhancers	Lung	lung
24	chr2:99524800-99526600	Enhancers	Psoas Muscle	Psoas
25	chr2:99524800-99526600	Enhancers	HSMMtube	muscle
26	chr2:99524800-99526800	Enhancers	Fetal Lung	lung
27	chr2:99524800-99527000	Enhancers	HSMM	muscle
28	chr2:99525000-99526400	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr2:99525000-99526400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:99525000-99526600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:99525000-99526600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:99525000-99526600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:99525000-99526600	Enhancers	Fetal Kidney	kidney
34	chr2:99525000-99526600	Enhancers	NH-A	brain
35	chr2:99525000-99526800	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr2:99525000-99526800	Enhancers	Fetal Stomach	stomach
37	chr2:99525200-99526400	Enhancers	Stomach Smooth Muscle	stomach
38	chr2:99525200-99526600	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr2:99525200-99526600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:99525200-99526600	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr2:99525200-99526600	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr2:99525200-99526600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:99525200-99526800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr2:99525200-99530600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr2:99525400-99526400	Enhancers	Primary T cells from cord blood	blood
46	chr2:99525400-99526400	Enhancers	NHDF-Ad	bronchial
47	chr2:99525400-99526600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:99525600-99526400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:99525600-99526400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:99525600-99526400	Enhancers	Colonic Mucosa	Colon

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