Variant report

Variant	rs10194496
Chromosome Location	chr2:112820462-112820463
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:112819853..112822054-chr2:113032254..113034904,2	K562	blood:
2	chr2:112818714..112821811-chr2:112824906..112828402,3	MCF-7	breast:
3	chr2:112817222..112820488-chr2:112832870..112835858,3	K562	blood:
4	chr2:112815166..112819031-chr2:112819758..112824247,10	K562	blood:
5	chr2:112819853..112822775-chr2:113032254..113034954,2	K562	blood:
6	chr2:112819134..112821985-chr2:112825483..112827864,2	K562	blood:

Variant related genes	Relation type
ENSG00000188177	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10169022	0.82[JPT][hapmap]
rs10176769	0.91[JPT][hapmap]
rs10192728	0.81[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs11123109	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11692445	0.81[JPT][hapmap]
rs13001162	0.82[JPT][hapmap]
rs4632347	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4848971	0.82[JPT][hapmap]
rs4848973	0.82[JPT][hapmap]
rs4848979	0.91[JPT][hapmap]
rs4848980	0.90[JPT][hapmap]
rs66990408	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6722814	0.91[JPT][hapmap]
rs6748256	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.98[LWK][hapmap];0.88[MEX][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv1013218	chr2:112645633-112908416	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv3333591	chr2:112669320-112892618	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1002027	chr2:112679182-112861534	Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1014787	chr2:112679182-112908416	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv535893	chr2:112679182-112908416	Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10194496	BCL2L11	cis	parietal	SCAN
rs10194496	TMEM87B	cis	parietal	SCAN
rs10194496	IL1F10	cis	parietal	SCAN
rs10194496	FBLN7	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112814200-112821000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:112814200-112827000	Weak transcription	Psoas Muscle	Psoas
3	chr2:112814200-112835400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:112814200-112849800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:112814200-112859800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:112814400-112821400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:112814400-112831600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:112814600-112820600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:112814600-112820600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:112814600-112821600	Weak transcription	Fetal Brain Female	brain
11	chr2:112814600-112829400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:112814800-112820600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:112814800-112823800	Weak transcription	Brain Substantia Nigra	brain
14	chr2:112814800-112826800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr2:112814800-112832200	Weak transcription	A549	lung
16	chr2:112814800-112842000	Weak transcription	Fetal Heart	heart
17	chr2:112815000-112822000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:112815000-112824000	Weak transcription	Brain Germinal Matrix	brain
19	chr2:112815200-112820600	Weak transcription	Adipose Nuclei	Adipose
20	chr2:112815200-112822200	Weak transcription	Pancreas	Pancrea
21	chr2:112815200-112823200	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:112815200-112823600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:112815200-112823600	Weak transcription	Fetal Brain Male	brain
24	chr2:112815200-112833200	Weak transcription	Hela-S3	cervix
25	chr2:112815800-112822600	Strong transcription	HSMM	muscle
26	chr2:112816000-112825000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:112816000-112833800	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:112816200-112821000	Weak transcription	NHLF	lung
29	chr2:112816400-112822200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:112816400-112823000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr2:112816400-112827200	Strong transcription	Fetal Muscle Trunk	muscle
32	chr2:112816400-112829600	Strong transcription	Placenta	Placenta
33	chr2:112816600-112820600	Weak transcription	Left Ventricle	heart
34	chr2:112816600-112820600	Weak transcription	Spleen	Spleen
35	chr2:112816600-112820800	Weak transcription	Gastric	stomach
36	chr2:112816600-112822200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:112816600-112825200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr2:112816600-112834200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr2:112816600-112866200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr2:112816800-112823200	Strong transcription	Osteobl	bone
41	chr2:112816800-112871400	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr2:112817000-112827000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:112817000-112827400	Strong transcription	Fetal Stomach	stomach
44	chr2:112817000-112830200	Strong transcription	Fetal Muscle Leg	muscle
45	chr2:112817200-112820600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:112817200-112821000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr2:112817200-112822600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:112817200-112822800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:112817200-112823000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:112817200-112823000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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