Variant report

Variant	rs2179174
Chromosome Location	chr6:28238969-28238970
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	chr6:28232169..28234255-chr6:28237329..28239836,2	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12000	1.00[CEU][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16893889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16893947	0.84[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16893970	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1936364	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56152789	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7772827	0.90[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2179174	AL022393.7	cis	Thyroid	GTEx
rs2179174	ZKSCAN3	cis	parietal	SCAN
rs2179174	HIST1H4C	cis	parietal	SCAN
rs2179174	ZNF165	cis	parietal	SCAN
rs2179174	ZNF187	cis	cerebellum	SCAN
rs2179174	ZNF323	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28235200-28239600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:28235400-28239600	Weak transcription	Gastric	stomach
3	chr6:28235400-28249000	Weak transcription	Small Intestine	intestine
4	chr6:28235600-28239200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:28235600-28239200	Weak transcription	Lung	lung
6	chr6:28235600-28239600	Weak transcription	Aorta	Aorta
7	chr6:28235600-28239600	Weak transcription	Esophagus	oesophagus
8	chr6:28235600-28239600	Weak transcription	Left Ventricle	heart
9	chr6:28235600-28239800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:28235600-28239800	Weak transcription	Pancreas	Pancrea
11	chr6:28235600-28240000	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr6:28235600-28243400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:28235600-28249000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:28235600-28249000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:28235800-28239200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:28235800-28239200	Weak transcription	Right Ventricle	heart
17	chr6:28236000-28239200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:28236000-28239200	Weak transcription	Fetal Intestine Small	intestine
19	chr6:28236000-28239200	Weak transcription	Spleen	Spleen
20	chr6:28236000-28239400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:28236000-28239600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:28236000-28239600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr6:28236000-28239600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr6:28236000-28239600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr6:28236000-28239600	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:28236000-28239600	Weak transcription	Placenta	Placenta
27	chr6:28236000-28239600	Weak transcription	Fetal Thymus	thymus
28	chr6:28236000-28239600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr6:28236000-28239600	Weak transcription	Thymus	Thymus
30	chr6:28236000-28239600	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr6:28236000-28239800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr6:28236000-28239800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr6:28236000-28239800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:28236200-28239200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:28236200-28239200	Weak transcription	Brain Anterior Caudate	brain
36	chr6:28236200-28239400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr6:28236200-28239600	Weak transcription	Primary B cells from cord blood	blood
38	chr6:28236200-28239600	Weak transcription	Brain Substantia Nigra	brain
39	chr6:28236200-28239600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr6:28236200-28239600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr6:28236200-28239600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr6:28236200-28239800	Weak transcription	Liver	Liver
43	chr6:28236200-28239800	Weak transcription	Colonic Mucosa	Colon
44	chr6:28236200-28239800	Weak transcription	HSMM	muscle
45	chr6:28236200-28240000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr6:28236200-28241800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr6:28236200-28247400	Weak transcription	Stomach Mucosa	stomach
48	chr6:28236200-28248000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr6:28236200-28249400	Weak transcription	Fetal Heart	heart
50	chr6:28236400-28239200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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