Variant report

Variant	rs12471315
Chromosome Location	chr2:173329965-173329966
allele	A/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	MXI1	chr2:173329836-173331023	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr2:173329920-173330070	AG10803	skin:	n/a	n/a
3	CTCF	chr2:173329937-173331141	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr2:173329954-173331103	A549	lung:	n/a	n/a
5	RAD21	chr2:173329927-173331183	SK-N-SH	brain:	n/a	n/a
6	STAT3	chr2:173329921-173329987	MCF10A-Er-Src	breast:	n/a	n/a
7	MYBL2	chr2:173329956-173330881	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172966254..172968915-chr2:173327645..173330223,2	MCF-7	breast:
2	chr2:173041440..173044413-chr2:173328538..173330490,2	MCF-7	breast:

Variant related genes	Relation type
ITGA6	TF binding region
ENSG00000115844	Chromatin interaction
ENSG00000236651	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1076597	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10930558	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12693001	0.81[JPT][hapmap]
rs2272499	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4972840	0.89[CEU][hapmap]
rs6743724	0.85[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173319200-173330600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr2:173321400-173356000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:173324000-173330200	Weak transcription	Psoas Muscle	Psoas
4	chr2:173324400-173330600	Enhancers	HUVEC	blood vessel
5	chr2:173324600-173330400	Enhancers	Primary hematopoietic stem cells	blood
6	chr2:173326000-173330000	Enhancers	HepG2	liver
7	chr2:173326000-173330600	Enhancers	Primary B cells from peripheral blood	blood
8	chr2:173326000-173330600	Enhancers	Fetal Intestine Large	intestine
9	chr2:173326000-173330600	Enhancers	Fetal Thymus	thymus
10	chr2:173326000-173330600	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr2:173326400-173330200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:173326400-173330200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:173326400-173340400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:173326600-173330600	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr2:173326800-173330000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:173327000-173330000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:173327000-173330400	Genic enhancers	Fetal Intestine Small	intestine
18	chr2:173327200-173330000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:173327200-173330000	Weak transcription	NH-A	brain
20	chr2:173327200-173330200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:173327200-173330600	Enhancers	Dnd41	blood
22	chr2:173327200-173353200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:173327400-173338600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:173327400-173345000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:173327600-173330600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:173327800-173330000	Weak transcription	Brain Anterior Caudate	brain
27	chr2:173327800-173330000	Weak transcription	Brain Substantia Nigra	brain
28	chr2:173327800-173330200	Enhancers	Colonic Mucosa	Colon
29	chr2:173327800-173330200	Enhancers	Duodenum Mucosa	Duodenum
30	chr2:173327800-173333200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:173327800-173370800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:173328000-173330000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:173328000-173330000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:173328000-173330000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:173328000-173330000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr2:173328000-173330200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr2:173328000-173330600	Enhancers	Stomach Mucosa	stomach
38	chr2:173328000-173335800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr2:173328200-173330000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr2:173328200-173330000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr2:173328200-173330200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr2:173328200-173330600	Enhancers	Placenta Amnion	Placenta Amnion
43	chr2:173328200-173331000	Genic enhancers	HMEC	breast
44	chr2:173328400-173330000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:173328400-173330200	Enhancers	Primary B cells from cord blood	blood
46	chr2:173328600-173330200	Weak transcription	Placenta	Placenta
47	chr2:173328600-173330600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:173328600-173330800	Enhancers	Primary T cells fromperipheralblood	blood
49	chr2:173328600-173331000	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr2:173328800-173330000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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