Variant report

Variant	rs7248
Chromosome Location	chr12:10375302-10375303
allele	A/C
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	chr12:10372534-10377685	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr12:10375288-10377085	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:10374583-10377702	IMR90	lung:	n/a	n/a
4	POLR2A	chr12:10372283-10377246	A549	lung:	n/a	n/a
5	POLR2A	chr12:10375221-10375318	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:10375194-10375552	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:10373969..10375781-chr12:10380719..10382478,2	K562	blood:

Variant related genes	Relation type
KLRD1	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10845076	0.88[AMR][1000 genomes]
rs10845099	0.84[LWK][hapmap]
rs2900384	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4764331	0.91[LWK][hapmap]
rs7970821	0.85[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1054811	chr12:10350587-10440005	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7248	GSG1	cis	cerebellum	SCAN
rs7248	CLEC12B	cis	lymphoblastoid	seeQTL
rs7248	CLEC12A	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10366800-10386600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:10368000-10375400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:10368400-10377000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:10368400-10378400	Weak transcription	Fetal Heart	heart
5	chr12:10368400-10378600	Weak transcription	Stomach Mucosa	stomach
6	chr12:10368400-10380200	Weak transcription	GM12878-XiMat	blood
7	chr12:10368400-10380400	Weak transcription	Dnd41	blood
8	chr12:10369000-10376000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:10369000-10376600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:10369000-10377800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:10369200-10377200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:10369400-10377000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:10369400-10377600	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr12:10370000-10377200	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:10370200-10376600	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr12:10370200-10377200	Strong transcription	Fetal Stomach	stomach
17	chr12:10370400-10376600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr12:10370600-10376600	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr12:10370600-10377000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:10370600-10377000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:10370600-10377200	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr12:10370600-10377200	Strong transcription	H9 Cell Line	embryonic stem cell
23	chr12:10370600-10377200	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:10370600-10377200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr12:10370600-10377200	Strong transcription	Stomach Smooth Muscle	stomach
26	chr12:10370600-10377600	Strong transcription	Fetal Muscle Leg	muscle
27	chr12:10370800-10376800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:10371200-10376800	Strong transcription	Placenta Amnion	Placenta Amnion
29	chr12:10371200-10377200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
30	chr12:10371200-10377600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:10371400-10376600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr12:10371400-10377600	Strong transcription	Ovary	ovary
33	chr12:10371600-10376400	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:10371600-10377000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:10371600-10377200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr12:10371600-10377200	Strong transcription	Lung	lung
37	chr12:10371600-10377600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:10371800-10376200	Strong transcription	Fetal Thymus	thymus
39	chr12:10371800-10376400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
40	chr12:10371800-10376600	Strong transcription	Brain Germinal Matrix	brain
41	chr12:10371800-10376600	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:10371800-10377000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:10371800-10377000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr12:10371800-10377000	Strong transcription	Fetal Muscle Trunk	muscle
45	chr12:10371800-10377000	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr12:10371800-10377200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr12:10371800-10377200	Strong transcription	Fetal Brain Female	brain
48	chr12:10371800-10377200	Strong transcription	HSMMtube	muscle
49	chr12:10372000-10377200	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr12:10372200-10376400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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