Variant report

Variant	rs1233710
Chromosome Location	chr6:28215446-28215447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28198177..28200363-chr6:28214686..28217029,3	MCF-7	breast:
2	chr6:28116033..28118585-chr6:28214732..28216735,2	MCF-7	breast:
3	chr6:28206024..28209591-chr6:28211608..28215918,4	MCF-7	breast:
4	chr6:28214282..28215929-chr6:28234474..28235993,2	K562	blood:
5	chr6:28105200..28107128-chr6:28213873..28216450,2	K562	blood:
6	chr6:28214010..28215989-chr6:28244220..28246333,2	MCF-7	breast:
7	chr6:28202226..28208942-chr6:28209296..28217649,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197062	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10484542	0.85[CEU][hapmap]
rs1416919	0.85[CEU][hapmap];0.80[MEX][hapmap]
rs1635	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16893827	0.85[CEU][hapmap]
rs16893917	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs16893929	0.82[AMR][1000 genomes]
rs16893973	0.85[CEU][hapmap]
rs16893975	0.85[CEU][hapmap];0.80[MEX][hapmap]
rs17720687	0.82[CEU][hapmap]
rs2159275	0.85[CEU][hapmap]
rs2299030	1.00[CEU][hapmap]
rs3800324	0.82[AMR][1000 genomes]
rs3800327	0.85[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4711167	0.85[CEU][hapmap];0.80[MEX][hapmap]
rs4713159	0.85[CEU][hapmap];0.80[MEX][hapmap]
rs723475	0.85[CEU][hapmap];0.80[MEX][hapmap]
rs723476	0.85[CEU][hapmap];0.80[MEX][hapmap]
rs742107	0.85[CEU][hapmap];0.80[MEX][hapmap]
rs758398	0.90[JPT][hapmap]
rs7750106	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7757215	0.85[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28193800-28218400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:28193800-28218400	Weak transcription	Stomach Mucosa	stomach
3	chr6:28201600-28219400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:28203000-28218400	Weak transcription	HUVEC	blood vessel
5	chr6:28211000-28216200	Strong transcription	Brain Hippocampus Middle	brain
6	chr6:28211000-28216800	Strong transcription	Brain Germinal Matrix	brain
7	chr6:28211000-28217200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:28211000-28217200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:28211000-28217600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:28211000-28217600	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr6:28211000-28217600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr6:28211000-28217600	Strong transcription	Placenta	Placenta
13	chr6:28211200-28216800	Strong transcription	Primary B cells from cord blood	blood
14	chr6:28211200-28217000	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:28211200-28217400	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:28211200-28217600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:28211400-28216200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:28211400-28216400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:28211400-28216400	Strong transcription	Primary B cells from peripheral blood	blood
20	chr6:28211400-28217000	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr6:28211600-28216200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:28211600-28216200	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr6:28211600-28216600	Strong transcription	Fetal Stomach	stomach
24	chr6:28211600-28216800	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:28211600-28217000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:28211600-28217000	Strong transcription	Liver	Liver
27	chr6:28211600-28217600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr6:28211600-28217600	Strong transcription	Fetal Muscle Trunk	muscle
29	chr6:28211600-28217600	Strong transcription	Left Ventricle	heart
30	chr6:28211600-28217600	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr6:28211600-28217600	Strong transcription	Stomach Smooth Muscle	stomach
32	chr6:28211600-28217800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:28211600-28218000	Strong transcription	Fetal Muscle Leg	muscle
34	chr6:28211800-28216000	Strong transcription	Fetal Brain Female	brain
35	chr6:28211800-28216400	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr6:28211800-28217200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:28211800-28217400	Strong transcription	Primary T cells from cord blood	blood
38	chr6:28211800-28217400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:28211800-28217600	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr6:28211800-28217800	Strong transcription	Fetal Thymus	thymus
41	chr6:28212000-28215800	Strong transcription	Dnd41	blood
42	chr6:28212000-28216200	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr6:28212000-28216200	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr6:28212000-28216200	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr6:28212000-28216400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr6:28212000-28216400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:28212000-28217000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr6:28212000-28217600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr6:28212000-28217600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:28212000-28217600	Strong transcription	Adipose Nuclei	Adipose

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