Variant report

Variant	rs12991192
Chromosome Location	chr2:74309666-74309667
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:74210985..74213488-chr2:74306326..74309716,4	MCF-7	breast:
2	chr2:74307941..74310204-chr2:74366126..74368255,2	K562	blood:
3	chr2:74230315..74232342-chr2:74308990..74310979,2	K562	blood:
4	chr2:74303366..74305130-chr2:74308677..74311311,2	K562	blood:

Variant related genes	Relation type
ENSG00000235499	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11683738	1.00[CHB][hapmap]
rs11898903	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12995468	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13002080	1.00[CHB][hapmap]
rs13005103	1.00[ASN][1000 genomes]
rs13011961	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13013211	1.00[ASN][1000 genomes]
rs13016198	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[ASN][1000 genomes]
rs13019449	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13027623	1.00[ASN][1000 genomes]
rs17676291	1.00[CHB][hapmap]
rs17725971	1.00[CHB][hapmap]
rs34136450	1.00[ASN][1000 genomes]
rs34201525	1.00[ASN][1000 genomes]
rs35592918	1.00[ASN][1000 genomes]
rs35609589	1.00[ASN][1000 genomes]
rs4270374	1.00[ASN][1000 genomes]
rs4374402	1.00[ASN][1000 genomes]
rs4422181	1.00[ASN][1000 genomes]
rs6712566	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713313	0.86[ASN][1000 genomes]
rs6717896	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6754218	1.00[ASN][1000 genomes]
rs71337722	1.00[ASN][1000 genomes]
rs71406850	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585240	0.85[CEU][hapmap]
rs7593050	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[ASN][1000 genomes]
rs7597388	1.00[ASN][1000 genomes]
rs870722	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	esv3584956	chr2:74197109-74317135	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv818048	chr2:74225434-74313080	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv874284	chr2:74283728-74348797	Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv874285	chr2:74283728-74355244	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12991192	SEMA4F	cis	parietal	SCAN
rs12991192	SLC4A5	cis	parietal	SCAN
rs12991192	AUP1	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74264800-74311000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr2:74265400-74315000	Weak transcription	HUVEC	blood vessel
3	chr2:74269800-74328000	Weak transcription	Psoas Muscle	Psoas
4	chr2:74275800-74317000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr2:74279200-74317000	Weak transcription	Small Intestine	intestine
6	chr2:74281800-74310200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr2:74282000-74319600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:74287400-74314000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:74287600-74310600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:74298400-74320600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:74299800-74332000	Strong transcription	Dnd41	blood
12	chr2:74299800-74333800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:74300000-74314200	Weak transcription	HMEC	breast
14	chr2:74300000-74333200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:74300800-74333600	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr2:74301800-74318000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:74303200-74310200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:74303200-74321000	Weak transcription	Fetal Brain Male	brain
19	chr2:74304600-74314000	Weak transcription	Stomach Mucosa	stomach
20	chr2:74305000-74316600	Weak transcription	Right Atrium	heart
21	chr2:74305800-74313200	Weak transcription	Fetal Heart	heart
22	chr2:74306000-74332400	Strong transcription	Fetal Intestine Small	intestine
23	chr2:74306400-74332000	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr2:74306600-74311400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
25	chr2:74306800-74311200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:74306800-74311400	Strong transcription	Fetal Stomach	stomach
27	chr2:74306800-74311400	Strong transcription	NHEK	skin
28	chr2:74306800-74311600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr2:74306800-74316800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:74306800-74323000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr2:74306800-74323000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:74306800-74323600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr2:74306800-74323600	Strong transcription	Brain Germinal Matrix	brain
34	chr2:74306800-74323600	Strong transcription	Fetal Intestine Large	intestine
35	chr2:74306800-74330400	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr2:74307000-74310800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr2:74307000-74324200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:74307000-74332600	Strong transcription	Primary T cells from cord blood	blood
39	chr2:74307200-74311200	Strong transcription	Lung	lung
40	chr2:74307200-74311800	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr2:74307200-74331800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:74307200-74332600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:74307200-74333000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr2:74307400-74311000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:74307400-74311200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:74307400-74311200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:74307400-74311800	Strong transcription	HepG2	liver
48	chr2:74307400-74314800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr2:74307400-74322600	Strong transcription	Fetal Brain Female	brain
50	chr2:74307400-74323600	Strong transcription	Primary B cells from peripheral blood	blood

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