Variant report

Variant	rs2035545
Chromosome Location	chr12:57477431-57477432
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBL1XR1	chr12:57477384-57477546	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57476897..57479666-chr12:57576067..57577675,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STAT6-1	chr12:57477095-57478488	XLOC_010097
2	lnc-STAT6-1	chr12:57477184-57478550	XLOC_010097

Variant related genes	Relation type
TMEM194A	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1044939	0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10506350	0.86[JPT][hapmap]
rs10506351	0.88[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1072670	0.88[JPT][hapmap]
rs11834851	0.88[JPT][hapmap]
rs12099695	0.86[JPT][hapmap]
rs1552245	0.88[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs17119301	0.86[JPT][hapmap]
rs17119327	0.88[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap]
rs17119330	0.88[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap]
rs17119344	0.88[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs17119352	0.81[ASN][1000 genomes]
rs17119386	0.88[CEU][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs17119388	0.88[CEU][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs17119390	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs17119407	0.88[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17119416	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17119418	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2233267	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2270736	0.88[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs2270737	0.88[CEU][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2270739	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs2279373	0.86[JPT][hapmap]
rs2279743	0.86[JPT][hapmap]
rs2371717	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs3024974	1.00[CEU][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3024975	1.00[CEU][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34762603	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35493121	0.86[JPT][hapmap]
rs35937600	1.00[ASN][1000 genomes]
rs3759134	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3759135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3782329	0.82[CEU][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs3782330	0.88[CEU][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs3803018	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs4016338	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs4039	0.88[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4143085	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs56128678	0.83[ASN][1000 genomes]
rs56270558	0.83[ASN][1000 genomes]
rs56354404	0.83[ASN][1000 genomes]
rs57056392	0.82[ASN][1000 genomes]
rs58389529	0.81[ASN][1000 genomes]
rs61504157	0.82[ASN][1000 genomes]
rs66741626	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7135297	0.89[ASN][1000 genomes]
rs7136770	0.86[JPT][hapmap]
rs7298475	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73114437	0.81[ASN][1000 genomes]
rs73114446	0.81[ASN][1000 genomes]
rs73114452	0.81[ASN][1000 genomes]
rs73114457	0.83[ASN][1000 genomes]
rs73114459	0.83[ASN][1000 genomes]
rs73114467	0.83[ASN][1000 genomes]
rs73114468	0.83[ASN][1000 genomes]
rs73114472	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73116494	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73116501	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73118413	0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73118416	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73118418	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73118432	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs733629	0.88[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap]
rs746049	0.86[JPT][hapmap]
rs755221	0.83[ASN][1000 genomes]
rs7961920	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7962771	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7972615	0.88[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap]
rs901068	0.86[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57472600-57479000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:57472600-57479600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:57472600-57479600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:57472600-57479600	Weak transcription	Gastric	stomach
5	chr12:57472600-57480000	Weak transcription	Aorta	Aorta
6	chr12:57472800-57479000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:57473200-57479000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr12:57473200-57479400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr12:57473200-57479400	Weak transcription	Brain Germinal Matrix	brain
10	chr12:57473200-57480000	Weak transcription	Right Atrium	heart
11	chr12:57473400-57479400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:57473600-57479000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:57473600-57479000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:57473600-57479000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:57473600-57479400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:57473600-57479600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr12:57473600-57479600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:57473800-57478200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:57473800-57478200	Weak transcription	Fetal Intestine Small	intestine
20	chr12:57473800-57478600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr12:57473800-57478800	Weak transcription	Fetal Intestine Large	intestine
22	chr12:57473800-57478800	Weak transcription	Fetal Lung	lung
23	chr12:57473800-57479000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:57473800-57479000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:57473800-57479000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:57473800-57479000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr12:57473800-57479000	Weak transcription	Fetal Muscle Leg	muscle
28	chr12:57473800-57479000	Weak transcription	Fetal Thymus	thymus
29	chr12:57473800-57479000	Weak transcription	NHDF-Ad	bronchial
30	chr12:57473800-57479200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr12:57473800-57479200	Weak transcription	HMEC	breast
32	chr12:57473800-57479200	Weak transcription	NHLF	lung
33	chr12:57473800-57479400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr12:57473800-57479600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:57473800-57479600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr12:57473800-57479600	Weak transcription	Osteobl	bone
37	chr12:57473800-57479800	Weak transcription	Primary B cells from cord blood	blood
38	chr12:57473800-57479800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr12:57473800-57479800	Weak transcription	HepG2	liver
40	chr12:57474000-57479000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:57474000-57479000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr12:57474000-57479000	Weak transcription	Fetal Kidney	kidney
43	chr12:57474000-57479000	Weak transcription	Fetal Stomach	stomach
44	chr12:57474000-57479200	Weak transcription	Colon Smooth Muscle	Colon
45	chr12:57474000-57479200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr12:57474000-57479400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:57474000-57479400	Weak transcription	Hela-S3	cervix
48	chr12:57474200-57479200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr12:57474200-57479400	Weak transcription	Primary T cells from cord blood	blood
50	chr12:57474800-57478200	Weak transcription	Placenta	Placenta

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