Variant report

Variant	rs12197240
Chromosome Location	chr6:143175609-143175610
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	chr6:143171301..143176697-chr6:143264648..143267813,7	MCF-7	breast:
2	chr6:143173616..143176330-chr6:143177113..143179367,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000010818	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12190352	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194370	0.84[AFR][1000 genomes]
rs12194419	0.83[AMR][1000 genomes]
rs12203103	1.00[JPT][hapmap];0.84[MKK][hapmap];0.84[AFR][1000 genomes]
rs12216122	1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs199240	1.00[JPT][hapmap]
rs200143	1.00[JPT][hapmap]
rs200145	1.00[JPT][hapmap]
rs200148	1.00[JPT][hapmap]
rs55795539	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62430706	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62430708	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763535	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[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	nsv830829	chr6:143058408-143218077	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv538459	chr6:143165802-143360098	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143167200-143177000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr6:143167800-143176600	Enhancers	Primary T cells from cord blood	blood
3	chr6:143168200-143176000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:143168400-143176200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr6:143168400-143177400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:143168400-143177600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:143168400-143178600	Weak transcription	Fetal Stomach	stomach
8	chr6:143168400-143179000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:143168400-143179400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:143168400-143188600	Weak transcription	Aorta	Aorta
11	chr6:143169200-143175800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:143169200-143178600	Weak transcription	Fetal Brain Female	brain
13	chr6:143169400-143176200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr6:143170800-143176200	Enhancers	Small Intestine	intestine
15	chr6:143171600-143175800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:143172000-143175800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:143172000-143179400	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr6:143172200-143176200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:143172200-143176800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:143172800-143175800	Weak transcription	Adipose Nuclei	Adipose
21	chr6:143172800-143177000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr6:143173000-143175800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:143173000-143176000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:143173000-143176200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr6:143173200-143175800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:143173200-143175800	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr6:143173200-143178000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr6:143173200-143182400	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:143173200-143188600	Weak transcription	Fetal Intestine Small	intestine
30	chr6:143173400-143179600	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr6:143173600-143177800	Enhancers	HSMMtube	muscle
32	chr6:143173600-143188200	Weak transcription	NHLF	lung
33	chr6:143173800-143176400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:143173800-143179600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr6:143174200-143176400	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr6:143174200-143176600	Enhancers	Fetal Muscle Leg	muscle
37	chr6:143174200-143176600	Enhancers	Placenta	Placenta
38	chr6:143174200-143176600	Enhancers	Fetal Thymus	thymus
39	chr6:143174200-143177000	Enhancers	Primary B cells from peripheral blood	blood
40	chr6:143174200-143179600	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr6:143174400-143176600	Enhancers	Muscle Satellite Cultured Cells	--
42	chr6:143174400-143176600	Enhancers	Left Ventricle	heart
43	chr6:143174400-143176600	Enhancers	Lung	lung
44	chr6:143174400-143176600	Enhancers	Psoas Muscle	Psoas
45	chr6:143174400-143176600	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr6:143174400-143177600	Enhancers	Thymus	Thymus
47	chr6:143174400-143178000	Enhancers	Brain Angular Gyrus	brain
48	chr6:143174400-143178000	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr6:143174400-143178200	Enhancers	Brain Hippocampus Middle	brain
50	chr6:143174400-143179600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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