Variant report

Variant	rs7310868
Chromosome Location	chr12:12317820-12317821
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12316415..12318730-chr12:12419208..12421283,2	MCF-7	breast:
2	chr12:12315377..12318046-chr12:12335015..12337960,2	K562	blood:
3	chr12:12317349..12320437-chr12:12321643..12324297,3	MCF-7	breast:
4	chr12:12317242..12319657-chr12:12322207..12324128,2	K562	blood:

Variant related genes	Relation type
ENSG00000070018	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11054765	1.00[JPT][hapmap]
rs11834619	0.80[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488505	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488506	1.00[CHB][hapmap]
rs7310632	1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[ASN][1000 genomes]
rs7310718	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7315313	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963810	1.00[CHB][hapmap]
rs7971789	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7972682	1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7980348	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv529005	chr12:12254756-12412795	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1050715	chr12:12293072-12383820	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7310868	GBP6	trans	lymphoblastoid	seeQTL
rs7310868	CLIC2	trans	lymphoblastoid	seeQTL
rs7310868	FAM171A1	trans	lymphoblastoid	seeQTL
rs7310868	IL18R1	trans	lymphoblastoid	seeQTL
rs7310868	CADM1	trans	lymphoblastoid	seeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12262400-12335600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:12269600-12343200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:12272200-12344600	Weak transcription	Primary B cells from cord blood	blood
4	chr12:12272400-12325200	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr12:12279800-12342800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:12281800-12335600	Weak transcription	Psoas Muscle	Psoas
7	chr12:12287400-12318200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:12288200-12342800	Weak transcription	K562	blood
9	chr12:12289400-12318200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:12297200-12318000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:12297600-12321400	Weak transcription	Gastric	stomach
12	chr12:12302000-12318000	Weak transcription	Stomach Mucosa	stomach
13	chr12:12302200-12325000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr12:12302200-12338400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr12:12303600-12318200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:12303800-12335600	Weak transcription	Right Ventricle	heart
17	chr12:12304000-12319800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr12:12304000-12353000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr12:12305400-12318000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:12306600-12318200	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:12306800-12325200	Weak transcription	Small Intestine	intestine
22	chr12:12309600-12318000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:12310000-12321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr12:12312000-12325000	Weak transcription	Aorta	Aorta
25	chr12:12312000-12325000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr12:12312000-12332600	Weak transcription	Dnd41	blood
27	chr12:12312000-12350600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr12:12312200-12325000	Weak transcription	HMEC	breast
29	chr12:12312200-12334000	Weak transcription	Pancreas	Pancrea
30	chr12:12312200-12334600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:12312200-12338000	Weak transcription	Brain Germinal Matrix	brain
32	chr12:12312200-12355800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:12312200-12362000	Weak transcription	Hela-S3	cervix
34	chr12:12312400-12319200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:12312400-12325200	Weak transcription	Primary T cells from cord blood	blood
36	chr12:12312400-12332400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr12:12312400-12332600	Weak transcription	Fetal Thymus	thymus
38	chr12:12312800-12324800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr12:12312800-12337600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr12:12313800-12325000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr12:12314000-12318000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr12:12314000-12318000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:12314000-12318000	Weak transcription	HSMMtube	muscle
44	chr12:12314000-12325000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:12314000-12331400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:12314000-12333200	Weak transcription	NH-A	brain
47	chr12:12314000-12335600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr12:12314000-12336000	Weak transcription	Adipose Nuclei	Adipose
49	chr12:12314200-12324800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr12:12314200-12324800	Weak transcription	NHEK	skin

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