Variant report

Variant	rs6591234
Chromosome Location	chr11:66943872-66943873
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66823382..66825002-chr11:66942751..66945603,2	MCF-7	breast:
2	chr11:66942292..66944561-chr11:66946334..66947954,2	MCF-7	breast:
3	chr11:66942498..66944506-chr11:66944828..66946334,2	MCF-7	breast:
4	chr11:66941075..66944065-chr11:66959296..66961684,2	K562	blood:
5	chr11:66938482..66941224-chr11:66943551..66945647,2	K562	blood:

Variant related genes	Relation type
ENSG00000173156	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10791900	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10896161	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11227687	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11227689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11227690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11227695	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11227696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11227697	0.81[ASN][1000 genomes]
rs11227701	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11227703	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11227713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11227715	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11227718	0.94[ASN][1000 genomes]
rs11227720	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11227722	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11227723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11227732	1.00[ASN][1000 genomes]
rs11227740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs11227744	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11227745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11227746	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11227750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11227752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11227755	1.00[JPT][hapmap]
rs11227770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12271777	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12273711	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12274774	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12282264	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12293866	0.86[ASN][1000 genomes]
rs17145414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28604372	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3730145	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs55936319	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61395951	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61891311	1.00[EUR][1000 genomes]
rs61891316	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61891317	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61891340	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61891342	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61891343	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61891344	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61891346	0.94[ASN][1000 genomes]
rs6591235	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7111473	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7127431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs72926981	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7927142	1.00[EUR][1000 genomes]
rs7946985	1.00[EUR][1000 genomes]
rs7947663	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9630209	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv532287	chr11:66784014-67023899	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6591234	SSH3	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66905600-66950400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:66907800-66953000	Weak transcription	Aorta	Aorta
3	chr11:66907800-66975000	Weak transcription	Pancreas	Pancrea
4	chr11:66918600-66947200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr11:66918800-66947400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr11:66918800-66968000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr11:66919400-66947200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr11:66919600-66950400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr11:66919800-66947200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr11:66919800-66947400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:66919800-66947400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr11:66919800-66949600	Weak transcription	Lung	lung
13	chr11:66920000-66947600	Weak transcription	Right Ventricle	heart
14	chr11:66920400-66947200	Weak transcription	Placenta	Placenta
15	chr11:66920400-66947400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr11:66920800-66949200	Weak transcription	Fetal Kidney	kidney
17	chr11:66921200-66945200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr11:66921200-66946800	Weak transcription	Ovary	ovary
19	chr11:66922600-66947200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:66923000-66947400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr11:66923200-66947400	Weak transcription	Thymus	Thymus
22	chr11:66925800-66945200	Weak transcription	Fetal Lung	lung
23	chr11:66926000-66950400	Weak transcription	Brain Germinal Matrix	brain
24	chr11:66926000-66966800	Weak transcription	Brain Angular Gyrus	brain
25	chr11:66926200-66948400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr11:66926200-66963800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr11:66928600-66945000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr11:66929000-66947600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr11:66929600-66947200	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr11:66930600-66947400	Weak transcription	Fetal Muscle Leg	muscle
31	chr11:66930800-66985600	Weak transcription	Small Intestine	intestine
32	chr11:66932400-66945200	Weak transcription	Fetal Intestine Large	intestine
33	chr11:66932400-66947200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr11:66932600-66947000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr11:66933400-66948600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr11:66934400-66947000	Weak transcription	Left Ventricle	heart
37	chr11:66934400-66948800	Weak transcription	Psoas Muscle	Psoas
38	chr11:66934400-66949200	Weak transcription	Esophagus	oesophagus
39	chr11:66934400-66950600	Weak transcription	Colonic Mucosa	Colon
40	chr11:66934400-66951000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr11:66935400-66947200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr11:66935800-66945000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr11:66935800-66945400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr11:66935800-66947200	Weak transcription	NHEK	skin
45	chr11:66935800-66949600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr11:66936000-66945400	Weak transcription	HSMM	muscle
47	chr11:66936200-66945000	Weak transcription	Dnd41	blood
48	chr11:66936200-66945000	Weak transcription	HUVEC	blood vessel
49	chr11:66936200-66945800	Weak transcription	NH-A	brain
50	chr11:66936200-66947000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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