Variant report

Variant	rs11728699
Chromosome Location	chr4:110649891-110649892
allele	G/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:110648642..110653205-chr4:110733223..110738599,11	K562	blood:
2	chr4:110361667..110363335-chr4:110648741..110650588,2	K562	blood:
3	chr4:110623047..110625582-chr4:110648264..110650027,2	K562	blood:
4	chr4:110636503..110639400-chr4:110648800..110651046,2	MCF-7	breast:
5	chr4:110622125..110626663-chr4:110647059..110653148,13	MCF-7	breast:
6	chr4:110629385..110631488-chr4:110647132..110649951,2	K562	blood:
7	chr4:110613405..110615968-chr4:110648212..110650472,2	K562	blood:
8	chr4:110648895..110652104-chr4:110733858..110738186,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000138794	Chromatin interaction
ENSG00000109534	Chromatin interaction
ENSG00000272795	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10004377	0.89[ASW][hapmap];0.92[CEU][hapmap];0.84[YRI][hapmap]
rs11938222	0.84[JPT][hapmap]
rs13117504	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1541373	0.89[ASW][hapmap];0.85[CEU][hapmap]
rs2301717	0.89[ASW][hapmap];0.85[CEU][hapmap]
rs3181187	0.85[CEU][hapmap];0.84[YRI][hapmap]
rs4698780	0.85[LWK][hapmap]
rs4698782	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5030535	0.85[CEU][hapmap];0.83[YRI][hapmap]
rs5030539	0.85[CEU][hapmap]
rs6533444	0.82[LWK][hapmap]
rs6533451	0.89[ASW][hapmap];0.85[CEU][hapmap]
rs6831917	0.89[ASW][hapmap];0.85[CEU][hapmap]
rs6854876	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72674868	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7439493	1.00[ASW][hapmap];0.89[CEU][hapmap];0.96[GIH][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7674356	0.89[ASW][hapmap];0.85[CEU][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs7694620	0.89[ASW][hapmap];0.85[CEU][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs9992400	0.85[CEU][hapmap];0.84[YRI][hapmap]
rs9995011	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv595142	chr4:110609481-110656730	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv4463	chr4:110647731-110693125	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11728699	CASP6	cis	parietal	SCAN
rs11728699	CASP6	cis	cerebellum	SCAN
rs11728699	LARP7	cis	parietal	SCAN
rs11728699	RRH	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110625000-110650400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:110625000-110650400	Weak transcription	Spleen	Spleen
3	chr4:110625200-110650200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:110625200-110650200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:110635000-110650400	Weak transcription	Gastric	stomach
6	chr4:110635400-110650000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr4:110635800-110650000	Weak transcription	Right Ventricle	heart
8	chr4:110635800-110650400	Weak transcription	Lung	lung
9	chr4:110638200-110650000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr4:110638200-110650200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr4:110638400-110650000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr4:110638600-110650200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:110638600-110650400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr4:110638800-110650000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr4:110639000-110650400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr4:110644200-110650000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:110644200-110650000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr4:110648600-110650200	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr4:110648800-110650000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr4:110648800-110650000	Enhancers	HSMM	muscle
21	chr4:110648800-110652000	Active TSS	K562	blood
22	chr4:110649000-110650000	Enhancers	A549	lung
23	chr4:110649000-110650000	Flanking Active TSS	HSMMtube	muscle
24	chr4:110649000-110650200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr4:110649000-110650200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:110649000-110651800	Active TSS	Fetal Intestine Large	intestine
27	chr4:110649000-110652000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr4:110649000-110652000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:110649000-110652200	Active TSS	H1 Cell Line	embryonic stem cell
30	chr4:110649000-110652200	Active TSS	H9 Cell Line	embryonic stem cell
31	chr4:110649000-110652200	Active TSS	Fetal Intestine Small	intestine
32	chr4:110649200-110650000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr4:110649200-110650000	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr4:110649200-110650000	Enhancers	Fetal Brain Male	brain
35	chr4:110649200-110650600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr4:110649200-110650600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:110649200-110650800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:110649200-110650800	Flanking Active TSS	Liver	Liver
39	chr4:110649200-110651000	Flanking Active TSS	Dnd41	blood
40	chr4:110649200-110652000	Active TSS	Rectal Smooth Muscle	rectum
41	chr4:110649200-110652400	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr4:110649400-110650000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:110649400-110650000	Enhancers	Brain Anterior Caudate	brain
44	chr4:110649400-110650000	Weak transcription	Ovary	ovary
45	chr4:110649400-110650000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr4:110649400-110650000	Enhancers	HUVEC	blood vessel
47	chr4:110649400-110650000	Flanking Active TSS	NHDF-Ad	bronchial
48	chr4:110649400-110650200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr4:110649400-110650200	Enhancers	Colon Smooth Muscle	Colon
50	chr4:110649400-110650200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland

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