Variant report

Variant	rs10202029
Chromosome Location	chr2:190446284-190446285
allele	C/T
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	POLR2A	chr2:190444967-190446333	H1-neurons	neurons:	n/a	n/a
2	HDAC2	chr2:190446024-190446340	HepG2	liver:	n/a	chr2:190446111-190446125
3	TAL1	chr2:190445583-190447295	K562	blood:	n/a	chr2:190446828-190446846
4	HMGN3	chr2:190445150-190446945	K562	blood:	n/a	n/a
5	RAD21	chr2:190446152-190446750	H1-hESC	embryonic stem cell:	n/a	n/a
6	TEAD4	chr2:190446031-190446791	H1-hESC	embryonic stem cell:	n/a	n/a
7	HNF4A	chr2:190445988-190446347	HepG2	liver:	n/a	chr2:190446184-190446199 chr2:190446157-190446172
8	TCF12	chr2:190446075-190446494	H1-hESC	embryonic stem cell:	n/a	n/a
9	TBP	chr2:190444906-190447343	K562	blood:	n/a	n/a
10	CTBP2	chr2:190444952-190446826	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr2:190446200-190446350	GM12871	blood:	n/a	n/a
12	HEY1	chr2:190445207-190446352	HepG2	liver:	n/a	chr2:190445659-190445674 chr2:190445648-190445663
13	TBL1XR1	chr2:190446237-190447099	K562	blood:	n/a	n/a
14	POLR2A	chr2:190446092-190446349	H1-hESC	embryonic stem cell:	n/a	n/a
15	MYC	chr2:190446140-190447379	K562	blood:	n/a	chr2:190446376-190446385 chr2:190446372-190446382
16	EP300	chr2:190446006-190447605	K562	blood:	n/a	chr2:190447570-190447584 chr2:190447363-190447377 chr2:190446895-190446909 chr2:190447590-190447604
17	MBD4	chr2:190445539-190446352	HepG2	liver:	n/a	n/a
18	CCNT2	chr2:190445363-190446970	K562	blood:	n/a	chr2:190446828-190446848 chr2:190446371-190446380
19	PML	chr2:190446169-190447123	K562	blood:	n/a	n/a
20	CHD2	chr2:190446162-190446426	H1-hESC	embryonic stem cell:	n/a	chr2:190446369-190446379
21	POLR2A	chr2:190444982-190447214	K562	blood:	n/a	n/a
22	YY1	chr2:190446044-190446366	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr2:190444941-190446398	H1-neurons	neurons:	n/a	n/a
24	TBL1XR1	chr2:190446207-190447408	K562	blood:	n/a	n/a
25	YY1	chr2:190445168-190446411	HepG2	liver:	n/a	chr2:190445850-190445864 chr2:190446371-190446380
26	ZMIZ1	chr2:190445083-190447504	K562	blood:	n/a	n/a
27	RFX5	chr2:190446275-190446286	HepG2	liver:	n/a	n/a
28	RXRA	chr2:190446273-190446616	H1-hESC	embryonic stem cell:	n/a	n/a
29	TEAD4	chr2:190446008-190447221	K562	blood:	n/a	n/a
30	GATA3	chr2:190446268-190446898	T-47D	breast:	n/a	chr2:190446835-190446848 chr2:190446838-190446846 chr2:190446828-190446845
31	POLR2A	chr2:190444897-190447250	K562	blood:	n/a	n/a
32	NR2F2	chr2:190445997-190447163	K562	blood:	n/a	n/a
33	POLR2A	chr2:190444227-190448816	PBDE	blood:	n/a	n/a
34	GATA1	chr2:190444265-190447639	PBDE	blood:	n/a	chr2:190446835-190446848 chr2:190444336-190444343 chr2:190446838-190446846 chr2:190444485-190444495 chr2:190446828-190446845
35	RCOR1	chr2:190444861-190447429	K562	blood:	n/a	n/a
36	POLR2A	chr2:190445009-190447207	K562	blood:	n/a	n/a
37	SP1	chr2:190446034-190446642	H1-hESC	embryonic stem cell:	n/a	chr2:190446369-190446380 chr2:190446370-190446379 chr2:190446370-190446379 chr2:190446370-190446380 chr2:190446371-190446380 chr2:190446370-190446380 chr2:190446369-190446381 chr2:190446369-190446381 chr2:190446370-190446384 chr2:190446601-190446608
38	POLR2A	chr2:190446274-190446296	HepG2	liver:	n/a	n/a
39	MAX	chr2:190444898-190446430	HepG2	liver:	n/a	chr2:190446376-190446385 chr2:190446372-190446382
40	CUX1	chr2:190446194-190446294	K562	blood:	n/a	n/a
41	POLR2A	chr2:190444989-190447536	K562	blood:	n/a	n/a
42	RCOR1	chr2:190446091-190446581	HepG2	liver:	n/a	n/a
43	UBTF	chr2:190445058-190447034	K562	blood:	n/a	n/a
44	RCOR1	chr2:190446177-190447180	K562	blood:	n/a	n/a
45	MAZ	chr2:190444975-190447075	K562	blood:	n/a	chr2:190446376-190446385 chr2:190446372-190446382
46	MAX	chr2:190444828-190446842	HepG2	liver:	n/a	chr2:190446376-190446385 chr2:190446372-190446382
47	HEY1	chr2:190446048-190447010	K562	blood:	n/a	n/a
48	HEY1	chr2:190444877-190446966	K562	blood:	n/a	chr2:190445659-190445674 chr2:190445648-190445663
49	GTF2F1	chr2:190446125-190446325	K562	blood:	n/a	n/a
50	POLR2A	chr2:190445012-190447126	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190305660..190307734-chr2:190445889..190448100,2	K562	blood:
2	chr2:190443338..190447714-chr2:190524367..190527732,5	K562	blood:

Variant related genes	Relation type
SLC40A1	TF binding region
ENSG00000138381	Chromatin interaction
ENSG00000115368	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11674773	1.00[JPT][hapmap]
rs11677198	1.00[JPT][hapmap]
rs11677494	1.00[JPT][hapmap]
rs11682165	1.00[JPT][hapmap]
rs11685775	1.00[JPT][hapmap]
rs11694976	1.00[JPT][hapmap]
rs12465339	1.00[JPT][hapmap]
rs17198934	1.00[JPT][hapmap]
rs4277558	1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190441600-190446400	Active TSS	Rectal Smooth Muscle	rectum
2	chr2:190442200-190446400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:190442200-190446400	Active TSS	Aorta	Aorta
4	chr2:190442200-190446600	Active TSS	Right Atrium	heart
5	chr2:190443200-190446400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:190443200-190446600	Active TSS	Brain Anterior Caudate	brain
7	chr2:190443200-190446600	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr2:190443600-190446400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:190443600-190446400	Active TSS	Ovary	ovary
10	chr2:190444000-190446400	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr2:190444000-190446600	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr2:190444200-190446600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
13	chr2:190444400-190446400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr2:190444400-190446400	Active TSS	Brain Substantia Nigra	brain
15	chr2:190444400-190446600	Active TSS	Psoas Muscle	Psoas
16	chr2:190444400-190446800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr2:190444600-190446400	Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr2:190444600-190446400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:190444600-190446400	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr2:190444600-190446400	Active TSS	HSMMtube	muscle
21	chr2:190444800-190446400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr2:190444800-190446400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr2:190444800-190446400	Active TSS	A549	lung
24	chr2:190444800-190446400	Active TSS	HSMM	muscle
25	chr2:190444800-190446800	Active TSS	Fetal Kidney	kidney
26	chr2:190445000-190446400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
27	chr2:190445000-190446400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:190445000-190446400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:190445000-190446400	Active TSS	Colon Smooth Muscle	Colon
30	chr2:190445000-190446600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
31	chr2:190445000-190447000	Active TSS	K562	blood
32	chr2:190445200-190446400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:190445200-190446400	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:190445200-190446400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr2:190445200-190446400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:190445200-190446600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
37	chr2:190445400-190446400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
38	chr2:190445400-190446400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr2:190445400-190446400	Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr2:190445400-190446800	Active TSS	Brain Cingulate Gyrus	brain
41	chr2:190445400-190447000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
42	chr2:190445600-190446400	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
43	chr2:190445800-190446400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
44	chr2:190445800-190446400	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
45	chr2:190445800-190446600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:190445800-190446600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:190445800-190446600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
48	chr2:190446000-190446400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
49	chr2:190446000-190446400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
50	chr2:190446000-190446400	Flanking Active TSS	Brain Germinal Matrix	brain

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