Variant report

Variant	rs16901846
Chromosome Location	chr6:28254988-28254989
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28245880..28256877-chr6:28299741..28307557,21	K562	blood:
2	chr6:28251868..28254160-chr6:28254261..28256025,2	MCF-7	breast:
3	chr6:28246849..28251135-chr6:28253254..28258623,13	K562	blood:

Variant related genes	Relation type
ENSG00000137338	Chromatin interaction
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10484404	0.89[CEU][hapmap]
rs1062169	0.89[CEU][hapmap]
rs1150697	0.80[CEU][hapmap]
rs1150699	0.80[CEU][hapmap]
rs1150704	0.80[CEU][hapmap]
rs1150714	1.00[CEU][hapmap]
rs11752073	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233664	0.80[CEU][hapmap]
rs1233665	0.80[CEU][hapmap]
rs1233666	0.80[CEU][hapmap]
rs1474589	1.00[CEU][hapmap]
rs16893817	0.80[CEU][hapmap]
rs16893937	1.00[CEU][hapmap];0.81[MKK][hapmap]
rs17312661	0.83[CHD][hapmap]
rs1736890	0.80[CEU][hapmap]
rs1890809	0.89[CEU][hapmap]
rs2232422	0.89[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs2232428	0.89[CEU][hapmap];0.83[CHD][hapmap]
rs2281043	1.00[CEU][hapmap]
rs2622315	0.89[CEU][hapmap]
rs3800325	1.00[CEU][hapmap]
rs6456811	1.00[CEU][hapmap]
rs6917759	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923170	1.00[CEU][hapmap]
rs6929559	0.89[CEU][hapmap]
rs7744788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7766356	0.83[CHD][hapmap]
rs7769054	0.80[CEU][hapmap]
rs993619	0.80[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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs16901846	HIST1H4C	cis	parietal	SCAN
rs16901846	ZSCAN23	cis	cerebellum	SCAN
rs16901846	PARD6B	trans	cerebellum	SCAN
rs16901846	ZSCAN23	cis	parietal	SCAN
rs16901846	ZNF165	cis	parietal	SCAN
rs16901846	ZNF323	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28249800-28272200	Weak transcription	Spleen	Spleen
2	chr6:28250000-28255000	Weak transcription	Esophagus	oesophagus
3	chr6:28250000-28258000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:28250000-28258600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:28250000-28277600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:28250000-28293800	Weak transcription	Gastric	stomach
7	chr6:28250200-28273800	Weak transcription	Thymus	Thymus
8	chr6:28250400-28265600	Weak transcription	Primary T cells from cord blood	blood
9	chr6:28250400-28278600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr6:28250600-28267000	Weak transcription	NHEK	skin
11	chr6:28250600-28270800	Weak transcription	Fetal Heart	heart
12	chr6:28250600-28280600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:28250800-28256400	Strong transcription	A549	lung
14	chr6:28250800-28257600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:28250800-28270000	Weak transcription	Psoas Muscle	Psoas
16	chr6:28250800-28276800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:28251000-28255200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:28251000-28255600	Strong transcription	Brain Substantia Nigra	brain
19	chr6:28251000-28258200	Strong transcription	Fetal Muscle Leg	muscle
20	chr6:28251000-28258600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:28251000-28258600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:28251000-28270800	Weak transcription	Colonic Mucosa	Colon
23	chr6:28251000-28273800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:28251000-28277200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr6:28251000-28278800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:28251200-28256600	Strong transcription	Fetal Lung	lung
27	chr6:28251200-28257200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr6:28251200-28257600	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:28251200-28258400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:28251200-28258400	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr6:28251200-28259000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:28251200-28259400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:28251400-28255600	Strong transcription	K562	blood
34	chr6:28251400-28256200	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr6:28251400-28256600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:28251400-28257400	Strong transcription	Adipose Nuclei	Adipose
37	chr6:28251400-28258000	Strong transcription	Fetal Brain Female	brain
38	chr6:28251400-28262200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:28251600-28256200	Strong transcription	Stomach Smooth Muscle	stomach
40	chr6:28251600-28257600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr6:28251600-28258200	Strong transcription	Colon Smooth Muscle	Colon
42	chr6:28251600-28258200	Strong transcription	Fetal Muscle Trunk	muscle
43	chr6:28251600-28258400	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr6:28251600-28258400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr6:28251600-28258400	Strong transcription	Primary hematopoietic stem cells	blood
46	chr6:28251600-28258400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr6:28251800-28255200	Strong transcription	Ovary	ovary
48	chr6:28251800-28256400	Strong transcription	Brain Cingulate Gyrus	brain
49	chr6:28251800-28257600	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr6:28251800-28257600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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