Variant report

Variant	rs3087401
Chromosome Location	chr2:100020945-100020946
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:100018210-100022039	Hela-S3	cervix:	n/a	n/a
2	MAX	chr2:100020762-100021303	MCF-7	breast:	n/a	n/a
3	REST	chr2:100020837-100021232	MCF-7	breast:	n/a	n/a
4	POLR2A	chr2:100017635-100023110	K562	blood:	n/a	n/a
5	POLR2A	chr2:100020857-100020988	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:100019759-100022575	A549	lung:	n/a	n/a
7	POLR2A	chr2:100018326-100023156	K562	blood:	n/a	n/a
8	MAX	chr2:100020836-100021332	MCF-7	breast:	n/a	n/a
9	POLR2A	chr2:100018189-100023050	GM12878	blood:	n/a	n/a
10	TCF7L2	chr2:100020913-100021210	MCF-7	breast:	n/a	n/a
11	POLR2A	chr2:100019578-100022515	HepG2	liver:	n/a	n/a
12	POLR2A	chr2:100020492-100022531	K562	blood:	n/a	n/a
13	POLR2A	chr2:100018281-100023537	GM12891	blood:	n/a	n/a
14	POLR2A	chr2:100020321-100022197	H1-hESC	embryonic stem cell:	n/a	n/a
15	GATA3	chr2:100020851-100021272	T-47D	breast:	n/a	n/a
16	POLR2A	chr2:100020485-100023490	GM12878	blood:	n/a	n/a
17	POLR2A	chr2:100020465-100021220	K562	blood:	n/a	n/a
18	POLR2A	chr2:100010038-100028424	K562	blood:	n/a	n/a
19	POLR2A	chr2:100020864-100021394	Hela-S3	cervix:	n/a	n/a
20	FOXA1	chr2:100020921-100021179	T-47D	breast:	n/a	n/a
21	POLR2A	chr2:100020451-100022641	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr2:100019568-100023005	HepG2	liver:	n/a	n/a
23	BCL3	chr2:100018227-100021181	K562	blood:	n/a	chr2:100020827-100020836
24	JUND	chr2:100020903-100021088	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr2:100011558-100023544	K562	blood:	n/a	n/a
26	POLR2A	chr2:100018257-100023444	K562	blood:	n/a	n/a
27	POLR2A	chr2:100020795-100022260	MCF-7	breast:	n/a	n/a
28	POLR2A	chr2:100017908-100023255	K562	blood:	n/a	n/a
29	SPI1	chr2:100020628-100020959	GM12891	blood:	n/a	chr2:100020827-100020836
30	REST	chr2:100020875-100021324	MCF-7	breast:	n/a	n/a
31	POLR2A	chr2:100018308-100023042	HepG2	liver:	n/a	n/a
32	POLR2A	chr2:100020000-100021213	K562	blood:	n/a	n/a
33	POLR2A	chr2:100017668-100024580	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr2:100020879-100022655	HL-60	blood:	n/a	n/a
35	ZNF217	chr2:100020862-100021294	MCF-7	breast:	n/a	n/a
36	POLR2A	chr2:100020433-100021028	GM12891	blood:	n/a	n/a
37	POLR2A	chr2:100020477-100022271	K562	blood:	n/a	n/a
38	SPI1	chr2:100020664-100020998	GM12891	blood:	n/a	chr2:100020827-100020836

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:99950906..99955641-chr2:100018668..100021744,4	MCF-7	breast:
2	chr2:100019781..100021613-chr2:100105810..100107711,2	MCF-7	breast:
3	chr2:100019322..100022368-chr2:100023817..100027425,5	K562	blood:
4	chr2:100019850..100022413-chr2:100104870..100107869,3	MCF-7	breast:
5	chr2:100018784..100022368-chr2:100023520..100027749,4	K562	blood:
6	chr2:100020586..100023216-chr2:100029196..100032155,3	MCF-7	breast:
7	chr2:100008715..100012637-chr2:100019428..100022260,4	K562	blood:

No data

Variant related genes	Relation type
REV1	TF binding region
ENSG00000273306	TF binding region
ENSG00000135945	Chromatin interaction
ENSG00000158417	Chromatin interaction
ENSG00000115514	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2707634	1.00[CHB][hapmap]
rs28369939	0.94[MEX][hapmap];0.90[AMR][1000 genomes]
rs28382960	1.00[CHB][hapmap]
rs28382961	1.00[CHB][hapmap]
rs3087396	1.00[CHB][hapmap]
rs3205290	1.00[CHB][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	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv524466	chr2:99952086-100031551	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1014604	chr2:99980851-100097884	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1006625	chr2:99984550-100096371	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	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	chr2:99999400-100056800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:100001000-100022000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:100004800-100023000	Strong transcription	Primary B cells from cord blood	blood
4	chr2:100004800-100044800	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr2:100005200-100049800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:100005600-100045400	Strong transcription	Primary T cells from cord blood	blood
7	chr2:100005800-100045200	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr2:100005800-100062600	Strong transcription	Dnd41	blood
9	chr2:100005800-100066000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:100006000-100023400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr2:100006000-100026200	Strong transcription	HUVEC	blood vessel
12	chr2:100006000-100034200	Strong transcription	GM12878-XiMat	blood
13	chr2:100006000-100046400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:100006000-100049600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:100006000-100050800	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr2:100006000-100051000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr2:100006000-100081200	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr2:100006200-100023600	Strong transcription	Fetal Thymus	thymus
19	chr2:100006200-100028600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:100006200-100046400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr2:100006200-100051400	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr2:100006400-100022600	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:100006400-100023000	Strong transcription	Primary hematopoietic stem cells	blood
24	chr2:100006400-100034200	Strong transcription	Fetal Brain Female	brain
25	chr2:100006400-100046600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:100006600-100022400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:100006600-100023000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:100006600-100023000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:100006600-100023000	Strong transcription	Thymus	Thymus
30	chr2:100006600-100023200	Strong transcription	K562	blood
31	chr2:100006600-100024000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr2:100006600-100024000	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:100006600-100042600	Strong transcription	Fetal Muscle Trunk	muscle
34	chr2:100006800-100021000	Strong transcription	NHEK	skin
35	chr2:100006800-100023200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:100006800-100024000	Strong transcription	Fetal Muscle Leg	muscle
37	chr2:100007000-100021200	Strong transcription	Fetal Lung	lung
38	chr2:100007000-100022600	Strong transcription	Brain Germinal Matrix	brain
39	chr2:100007000-100035400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:100007200-100026000	Strong transcription	HMEC	breast
41	chr2:100009000-100045000	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr2:100009400-100023000	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr2:100009400-100034200	Strong transcription	Stomach Smooth Muscle	stomach
44	chr2:100009800-100050000	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr2:100010000-100022200	Strong transcription	Rectal Smooth Muscle	rectum
46	chr2:100010000-100023600	Strong transcription	Colon Smooth Muscle	Colon
47	chr2:100010800-100023000	Strong transcription	Lung	lung
48	chr2:100012600-100021000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:100013800-100025800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr2:100014200-100023200	Strong transcription	Cortex derived primary cultured neurospheres	brain

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