Variant report

Variant	rs7137638
Chromosome Location	chr12:106893863-106893864
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:106892816..106895572-chr12:106907809..106909841,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CKAP4-2	chr12:106893854-106893960	NR_040246

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1004601	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10778482	0.86[ASN][1000 genomes]
rs12424092	0.81[ASN][1000 genomes]
rs1882413	0.85[CHB][hapmap]
rs2243506	0.80[CHB][hapmap];0.81[CHD][hapmap]
rs2244958	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs2245062	0.86[CHB][hapmap]
rs2250262	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs2254755	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs2288270	0.93[ASN][1000 genomes]
rs7137444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721438	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7303737	0.81[AMR][1000 genomes]
rs7313412	0.97[ASN][1000 genomes]
rs7315611	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	esv3435035	chr12:106765277-107015325	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv832510	chr12:106787730-106951140	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7137638	ANO1	trans	parietal	SCAN
rs7137638	STAB2	cis	parietal	SCAN
rs7137638	TCP11L2	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106828600-106905800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:106854400-106904800	Weak transcription	HSMM	muscle
3	chr12:106854600-106899800	Weak transcription	Fetal Thymus	thymus
4	chr12:106855800-106895600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr12:106855800-106896200	Weak transcription	Thymus	Thymus
6	chr12:106856800-106899400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr12:106858600-106895400	Weak transcription	Fetal Heart	heart
8	chr12:106865400-106895200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:106865400-106897800	Weak transcription	Spleen	Spleen
10	chr12:106865600-106894200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:106872600-106897800	Weak transcription	Psoas Muscle	Psoas
12	chr12:106884800-106899800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:106886200-106916400	Weak transcription	A549	lung
14	chr12:106887600-106895400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr12:106887600-106898000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:106887600-106907800	Weak transcription	Small Intestine	intestine
17	chr12:106887800-106895200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr12:106887800-106900200	Weak transcription	Fetal Brain Male	brain
19	chr12:106888000-106899800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr12:106888200-106894200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:106888200-106895400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr12:106888200-106895600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:106888200-106897800	Weak transcription	Fetal Brain Female	brain
24	chr12:106888200-106898000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr12:106888200-106899400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:106888200-106906800	Weak transcription	Brain Substantia Nigra	brain
27	chr12:106888800-106900400	Weak transcription	Colon Smooth Muscle	Colon
28	chr12:106889000-106899600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:106889200-106897200	Weak transcription	Stomach Mucosa	stomach
30	chr12:106889200-106903200	Weak transcription	HMEC	breast
31	chr12:106889200-106904600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr12:106889200-106905400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:106889400-106894800	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr12:106889400-106896800	Strong transcription	Adipose Nuclei	Adipose
35	chr12:106889400-106899600	Strong transcription	Fetal Stomach	stomach
36	chr12:106889400-106904000	Strong transcription	Primary T cells from cord blood	blood
37	chr12:106889400-106904600	Strong transcription	Liver	Liver
38	chr12:106889600-106896600	Strong transcription	Ovary	ovary
39	chr12:106889800-106894800	Strong transcription	Fetal Intestine Small	intestine
40	chr12:106889800-106895400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr12:106889800-106896400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:106889800-106899600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:106889800-106899800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr12:106889800-106900200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:106889800-106901600	Strong transcription	Fetal Muscle Leg	muscle
46	chr12:106890000-106895400	Weak transcription	NHLF	lung
47	chr12:106890000-106896600	Strong transcription	Placenta	Placenta
48	chr12:106890000-106896800	Strong transcription	Fetal Muscle Trunk	muscle
49	chr12:106890000-106904200	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr12:106890200-106899200	Strong transcription	Primary T helper cells fromperipheralblood	blood

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