Variant report

Variant	rs623173
Chromosome Location	chr11:77529528-77529529
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: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	chr11:77496983..77499630-chr11:77529279..77531478,2	MCF-7	breast:
2	chr11:77523579..77527566-chr11:77528400..77532529,6	K562	blood:
3	chr11:77520152..77525474-chr11:77528362..77532820,9	MCF-7	breast:
4	chr11:77515983..77518515-chr11:77527821..77530386,2	K562	blood:
5	chr11:77529037..77533619-chr11:77704156..77707997,11	MCF-7	breast:
6	chr11:77529444..77531772-chr11:77755912..77758450,3	MCF-7	breast:
7	chr11:77528492..77530104-chr11:77530430..77532147,2	MCF-7	breast:
8	chr11:77528468..77531025-chr11:77533622..77535888,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000151364	Chromatin interaction
ENSG00000219529	Chromatin interaction
ENSG00000149262	Chromatin interaction
ENSG00000048649	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10899399	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10899404	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11237244	0.82[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs11237249	1.00[ASW][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap]
rs11237263	0.82[EUR][1000 genomes]
rs11237280	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11237318	0.91[EUR][1000 genomes]
rs11600140	0.82[EUR][1000 genomes]
rs11600998	0.82[ASN][1000 genomes]
rs11603438	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11604207	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs11606549	0.89[EUR][1000 genomes]
rs11607512	0.84[MEX][hapmap]
rs12285765	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12286317	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs17752006	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17752458	0.84[MEX][hapmap]
rs1783544	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2154972	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs24356	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2508189	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34130561	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3824865	1.00[YRI][hapmap]
rs4322421	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4344516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs484363	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4945220	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs537811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56218634	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs588217	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs598071	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs614495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs621456	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623907	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs635195	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs636971	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs643388	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs648601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs648896	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650171	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs663674	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs667225	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs668701	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs670090	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs684813	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs687037	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs694845	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs695046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7122968	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7123080	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72945598	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72947625	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72947668	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72949616	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72949618	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7950873	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7951033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs947841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050891	chr11:77416645-77788002	Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1037292	chr11:77431583-77745934	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv541092	chr11:77431583-77745934	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949316	chr11:77454076-77769885	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs623173	INTS4	Cis_1M	lymphoblastoid	RTeQTL
rs623173	INTS4	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77475400-77530000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:77496000-77530200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:77503600-77529600	Weak transcription	Right Ventricle	heart
4	chr11:77509800-77530000	Weak transcription	NH-A	brain
5	chr11:77512000-77529600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr11:77512400-77530200	Weak transcription	Esophagus	oesophagus
7	chr11:77512400-77530600	Weak transcription	Lung	lung
8	chr11:77512600-77530600	Weak transcription	Spleen	Spleen
9	chr11:77512800-77529800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr11:77512800-77530400	Weak transcription	Gastric	stomach
11	chr11:77515400-77530000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr11:77516600-77530200	Weak transcription	HSMM	muscle
13	chr11:77518600-77530000	Weak transcription	Brain Substantia Nigra	brain
14	chr11:77518800-77530000	Weak transcription	Colonic Mucosa	Colon
15	chr11:77519000-77530000	Weak transcription	Stomach Mucosa	stomach
16	chr11:77520000-77530000	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr11:77521200-77529800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr11:77522400-77529800	Weak transcription	Fetal Kidney	kidney
19	chr11:77522800-77530000	Weak transcription	Adipose Nuclei	Adipose
20	chr11:77522800-77530200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr11:77523200-77529800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr11:77523200-77530000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr11:77523200-77530200	Weak transcription	Placenta	Placenta
24	chr11:77524800-77529600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr11:77524800-77529600	Weak transcription	Fetal Thymus	thymus
26	chr11:77524800-77530000	Weak transcription	Fetal Intestine Large	intestine
27	chr11:77524800-77530000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr11:77524800-77530000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr11:77525200-77530400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr11:77525800-77530000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr11:77526200-77529800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr11:77526200-77530000	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr11:77526200-77530000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr11:77526200-77530200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:77526200-77530200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr11:77526200-77530200	Weak transcription	Psoas Muscle	Psoas
37	chr11:77526200-77530200	Weak transcription	Right Atrium	heart
38	chr11:77526200-77530400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:77526400-77529600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr11:77526400-77529600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr11:77526400-77529600	Weak transcription	Fetal Muscle Leg	muscle
42	chr11:77526400-77530000	Weak transcription	Fetal Intestine Small	intestine
43	chr11:77526400-77530000	Weak transcription	A549	lung
44	chr11:77526400-77530200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr11:77526600-77530200	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr11:77526800-77529600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr11:77527000-77530200	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr11:77527000-77530200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr11:77527000-77530200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr11:77527200-77530000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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