Variant report

Variant	rs10849038
Chromosome Location	chr12:4437379-4437380
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:4426548..4433577-chr12:4433933..4442534,18	MCF-7	breast:
2	chr12:4427806..4430418-chr12:4436877..4438934,2	K562	blood:

Variant related genes	Relation type
ENSG00000078237	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10744641	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849039	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063099	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063156	1.00[JPT][hapmap]
rs11610220	1.00[JPT][hapmap]
rs11610225	1.00[JPT][hapmap]
rs11611403	1.00[JPT][hapmap]
rs11613495	1.00[JPT][hapmap]
rs2970822	1.00[JPT][hapmap]
rs2970823	1.00[JPT][hapmap]
rs2970828	1.00[JPT][hapmap]
rs4360766	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4414304	0.89[ASW][hapmap];1.00[LWK][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs4765778	0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs55896784	0.94[ASN][1000 genomes]
rs61909228	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61909230	1.00[ASN][1000 genomes]
rs61909234	0.89[ASN][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	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv468985	chr12:4423612-4473329	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv557122	chr12:4423612-4473329	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	nsv557123	chr12:4436632-4736569	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10849038	FOXJ2	cis	parietal	SCAN
rs10849038	USP5	cis	cerebellum	SCAN
rs10849038	LRTM2	cis	cerebellum	SCAN
rs10849038	KCNA6	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4431000-4439600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:4431200-4443400	Weak transcription	Aorta	Aorta
3	chr12:4431200-4444600	Weak transcription	HSMMtube	muscle
4	chr12:4431200-4446400	Weak transcription	Fetal Stomach	stomach
5	chr12:4431200-4446800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:4431200-4461200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:4431200-4465800	Weak transcription	Psoas Muscle	Psoas
8	chr12:4431400-4445800	Weak transcription	Fetal Thymus	thymus
9	chr12:4431400-4446200	Weak transcription	Fetal Muscle Leg	muscle
10	chr12:4431400-4446400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr12:4431400-4446400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr12:4431600-4441000	Weak transcription	Brain Angular Gyrus	brain
13	chr12:4431600-4443200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:4431600-4443200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:4431600-4444800	Weak transcription	Brain Germinal Matrix	brain
16	chr12:4431600-4445800	Weak transcription	Liver	Liver
17	chr12:4431600-4446400	Weak transcription	Brain Anterior Caudate	brain
18	chr12:4431600-4446400	Weak transcription	Right Ventricle	heart
19	chr12:4431600-4446400	Weak transcription	Spleen	Spleen
20	chr12:4431600-4446800	Weak transcription	Fetal Intestine Small	intestine
21	chr12:4431600-4449400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:4431600-4460400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr12:4431600-4462200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:4431600-4463400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:4431600-4465000	Weak transcription	Pancreas	Pancrea
26	chr12:4431800-4438800	Weak transcription	HSMM	muscle
27	chr12:4431800-4441200	Weak transcription	Brain Substantia Nigra	brain
28	chr12:4431800-4443000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr12:4431800-4443200	Weak transcription	Adipose Nuclei	Adipose
30	chr12:4431800-4444400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:4431800-4444600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr12:4431800-4444800	Weak transcription	NH-A	brain
33	chr12:4431800-4446400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr12:4431800-4447200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:4432000-4438800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr12:4432000-4443200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:4432000-4443200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr12:4432000-4443800	Weak transcription	NHDF-Ad	bronchial
39	chr12:4432000-4444800	Weak transcription	Hela-S3	cervix
40	chr12:4432000-4448600	Weak transcription	Fetal Brain Female	brain
41	chr12:4432000-4450200	Weak transcription	Stomach Mucosa	stomach
42	chr12:4432200-4438800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:4432200-4438800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr12:4432200-4441800	Weak transcription	Osteobl	bone
45	chr12:4432200-4443200	Weak transcription	Brain Hippocampus Middle	brain
46	chr12:4432200-4445600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr12:4432200-4448000	Weak transcription	Right Atrium	heart
48	chr12:4432200-4463400	Weak transcription	Small Intestine	intestine
49	chr12:4432200-4463600	Weak transcription	Colonic Mucosa	Colon
50	chr12:4432400-4438600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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