Variant report

Variant	rs7311196
Chromosome Location	chr12:51719679-51719680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:51716760-51720317	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51475890..51478856-chr12:51719210..51722345,3	K562	blood:
2	chr12:51632967..51634708-chr12:51718961..51721755,2	K562	blood:
3	chr12:51417902..51420501-chr12:51719275..51722211,2	K562	blood:
4	chr12:51156096..51157796-chr12:51717451..51720427,2	MCF-7	breast:
5	chr12:51663552..51665090-chr12:51718894..51721818,2	MCF-7	breast:
6	chr12:51719185..51720763-chr12:51721819..51723856,2	MCF-7	breast:
7	chr12:51661913..51666807-chr12:51714627..51721165,8	MCF-7	breast:
8	chr12:51633168..51635077-chr12:51718759..51720463,2	MCF-7	breast:

No data

Variant related genes	Relation type
BIN2	TF binding region
ENSG00000183283	Chromatin interaction
ENSG00000170545	Chromatin interaction
ENSG00000110925	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000110911	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11341	1.00[CEU][hapmap]
rs12578771	0.89[EUR][1000 genomes]
rs12580302	0.84[EUR][1000 genomes]
rs12581282	0.89[EUR][1000 genomes]
rs17860277	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17860287	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17860296	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17860299	0.93[CEU][hapmap];1.00[TSI][hapmap]
rs17860302	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17860317	0.92[CEU][hapmap];0.93[TSI][hapmap]
rs17860346	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17860364	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17860365	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17860378	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17860380	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17860382	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17860387	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2288367	0.93[CEU][hapmap];0.83[GIH][hapmap];0.92[TSI][hapmap]
rs3782470	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs3858637	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap]
rs3969069	0.80[CEU][hapmap]
rs4761870	0.83[EUR][1000 genomes]
rs4761881	0.92[CEU][hapmap]
rs55901988	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57484374	0.84[EUR][1000 genomes]
rs58213562	0.89[EUR][1000 genomes]
rs58673573	0.86[EUR][1000 genomes]
rs60641385	0.89[EUR][1000 genomes]
rs60797544	0.85[EUR][1000 genomes]
rs61172662	0.84[EUR][1000 genomes]
rs61380773	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61570206	0.89[EUR][1000 genomes]
rs61605107	0.86[EUR][1000 genomes]
rs6580821	0.85[CEU][hapmap];0.92[TSI][hapmap]
rs7133314	0.84[CEU][hapmap];0.92[TSI][hapmap]
rs7135736	0.85[CEU][hapmap];0.92[TSI][hapmap]
rs7138394	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7308177	0.81[EUR][1000 genomes]
rs7312857	1.00[CEU][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs7316221	0.81[EUR][1000 genomes]
rs7316301	0.86[EUR][1000 genomes]
rs7316604	0.81[EUR][1000 genomes]
rs74093810	0.81[EUR][1000 genomes]
rs74093814	0.81[EUR][1000 genomes]
rs74093823	0.84[EUR][1000 genomes]
rs74093827	0.84[EUR][1000 genomes]
rs74093853	0.90[EUR][1000 genomes]
rs7954976	0.85[CEU][hapmap];0.92[TSI][hapmap]
rs7975715	0.81[EUR][1000 genomes]

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	nsv482304	chr12:51653496-51814917	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv469377	chr12:51690751-51733951	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv558877	chr12:51690751-51733951	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv832408	chr12:51696605-51871339	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7311196	FAM186B	cis	parietal	SCAN
rs7311196	COL2A1	cis	parietal	SCAN
rs7311196	ZNF641	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51711800-51721800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:51712800-51720200	Weak transcription	HMEC	breast
3	chr12:51713200-51720000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:51715000-51720000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:51715000-51720000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:51715000-51720000	Weak transcription	Hela-S3	cervix
7	chr12:51715000-51720000	Weak transcription	HSMM	muscle
8	chr12:51715000-51720200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:51715000-51720200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:51715000-51720200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr12:51715200-51719800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:51715200-51720000	Weak transcription	HSMMtube	muscle
13	chr12:51715200-51720200	Weak transcription	NHDF-Ad	bronchial
14	chr12:51715200-51720400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:51715200-51720600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:51715600-51720200	Weak transcription	A549	lung
17	chr12:51715600-51720800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:51715800-51720200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr12:51715800-51720400	Weak transcription	Fetal Lung	lung
20	chr12:51715800-51720400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr12:51715800-51720600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr12:51716000-51720600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr12:51717600-51721000	Weak transcription	Brain Substantia Nigra	brain
24	chr12:51717600-51722600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr12:51717800-51719800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr12:51717800-51720000	Weak transcription	Liver	Liver
27	chr12:51717800-51720000	Weak transcription	Brain Hippocampus Middle	brain
28	chr12:51717800-51720000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr12:51717800-51720400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr12:51717800-51722200	Weak transcription	Small Intestine	intestine
31	chr12:51718000-51720200	Weak transcription	Right Atrium	heart
32	chr12:51718000-51720400	Enhancers	Spleen	Spleen
33	chr12:51718000-51722400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr12:51718000-51724400	Enhancers	Primary B cells from peripheral blood	blood
35	chr12:51718000-51724400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:51718200-51720000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:51718200-51720200	Enhancers	K562	blood
38	chr12:51718200-51720600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:51718400-51719800	Weak transcription	Adipose Nuclei	Adipose
40	chr12:51718400-51720200	Enhancers	Primary hematopoietic stem cells	blood
41	chr12:51718400-51720200	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr12:51718400-51720400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:51718400-51720400	Weak transcription	Fetal Muscle Leg	muscle
44	chr12:51718400-51720400	Enhancers	GM12878-XiMat	blood
45	chr12:51718400-51720600	Enhancers	Primary B cells from cord blood	blood
46	chr12:51718400-51720600	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr12:51718400-51721200	Enhancers	Duodenum Mucosa	Duodenum
48	chr12:51718400-51722200	Enhancers	Primary T cells from cord blood	blood
49	chr12:51718400-51722400	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr12:51718400-51722400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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