Variant report

Variant	rs11756111
Chromosome Location	chr6:28252859-28252860
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

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	chr6:28248465..28251025-chr6:28251931..28253617,2	MCF-7	breast:
4	chr6:28252167..28254655-chr6:28264060..28265912,2	MCF-7	breast:
5	chr6:28188896..28191056-chr6:28251556..28253787,2	K562	blood:
6	chr6:28252016..28254141-chr6:28279359..28281399,2	K562	blood:
7	chr6:28249255..28252885-chr6:28315781..28319284,4	K562	blood:
8	chr6:28252150..28254646-chr6:28303488..28305026,3	K562	blood:
9	chr6:28249727..28254264-chr6:28300327..28304071,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000137338	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1062169	0.81[GIH][hapmap]
rs1150717	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1150719	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1150720	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11751702	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11757730	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11758148	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11758337	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11970439	1.00[JPT][hapmap]
rs13190937	0.91[LWK][hapmap]
rs13215804	0.84[LWK][hapmap]
rs1474589	0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs16893937	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17301128	1.00[JPT][hapmap]
rs17776284	1.00[JPT][hapmap]
rs1778477	1.00[CEU][hapmap];0.83[GIH][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1778478	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2185955	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2235358	1.00[JPT][hapmap]
rs2235359	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2281043	0.83[GIH][hapmap]
rs2299031	1.00[JPT][hapmap]
rs3800326	1.00[JPT][hapmap]
rs3800328	0.82[ASW][hapmap]
rs55831267	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6456811	0.83[GIH][hapmap]
rs6903652	1.00[JPT][hapmap]
rs6903823	0.88[JPT][hapmap]
rs6905368	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6912584	0.86[GIH][hapmap];1.00[JPT][hapmap]
rs6921919	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs6922111	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs6928773	0.82[ASW][hapmap]
rs73742542	0.82[EUR][1000 genomes]
rs7741443	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7769054	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs993619	0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11756111	HIST1H4C	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	chr6:28250000-28253200	Weak transcription	Placenta	Placenta
3	chr6:28250000-28254800	Weak transcription	Primary B cells from cord blood	blood
4	chr6:28250000-28254800	Weak transcription	Pancreas	Pancrea
5	chr6:28250000-28254800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr6:28250000-28255000	Weak transcription	Esophagus	oesophagus
7	chr6:28250000-28258000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:28250000-28258600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:28250000-28277600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr6:28250000-28293800	Weak transcription	Gastric	stomach
11	chr6:28250200-28273800	Weak transcription	Thymus	Thymus
12	chr6:28250400-28254000	Weak transcription	Brain Anterior Caudate	brain
13	chr6:28250400-28265600	Weak transcription	Primary T cells from cord blood	blood
14	chr6:28250400-28278600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:28250600-28253800	Weak transcription	HUVEC	blood vessel
16	chr6:28250600-28254800	Weak transcription	Fetal Thymus	thymus
17	chr6:28250600-28254800	Weak transcription	HMEC	breast
18	chr6:28250600-28254800	Weak transcription	NHDF-Ad	bronchial
19	chr6:28250600-28267000	Weak transcription	NHEK	skin
20	chr6:28250600-28270800	Weak transcription	Fetal Heart	heart
21	chr6:28250600-28280600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:28250800-28253400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:28250800-28256400	Strong transcription	A549	lung
24	chr6:28250800-28257600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:28250800-28270000	Weak transcription	Psoas Muscle	Psoas
26	chr6:28250800-28276800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr6:28251000-28253000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr6:28251000-28253600	Strong transcription	Osteobl	bone
29	chr6:28251000-28254200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:28251000-28255200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:28251000-28255600	Strong transcription	Brain Substantia Nigra	brain
32	chr6:28251000-28258200	Strong transcription	Fetal Muscle Leg	muscle
33	chr6:28251000-28258600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:28251000-28258600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:28251000-28270800	Weak transcription	Colonic Mucosa	Colon
36	chr6:28251000-28273800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr6:28251000-28277200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr6:28251000-28278800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr6:28251200-28253200	Weak transcription	Brain Hippocampus Middle	brain
40	chr6:28251200-28253200	Weak transcription	Hela-S3	cervix
41	chr6:28251200-28253400	Genic enhancers	Dnd41	blood
42	chr6:28251200-28254800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr6:28251200-28254800	Weak transcription	Fetal Intestine Small	intestine
44	chr6:28251200-28256600	Strong transcription	Fetal Lung	lung
45	chr6:28251200-28257200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:28251200-28257600	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr6:28251200-28258400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:28251200-28258400	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr6:28251200-28259000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:28251200-28259400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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