Variant report

Variant	rs1996794
Chromosome Location	chr11:9822596-9822597
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9814289..9816378-chr11:9820915..9822756,2	K562	blood:
2	chr11:9822472..9825243-chr11:9829711..9832940,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133812	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1032550	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10770060	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10770064	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10770065	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10840305	0.90[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10840306	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11042493	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12788348	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1553008	0.80[CEU][hapmap]
rs1875029	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1983002	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34328537	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34690050	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35401279	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs360136	0.94[JPT][hapmap]
rs360137	0.94[JPT][hapmap]
rs360147	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs360157	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs3751000	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs415895	0.89[JPT][hapmap]
rs429835	0.90[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4424662	0.80[CEU][hapmap]
rs4910063	0.90[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4910499	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs7126913	1.00[CEU][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7934930	0.82[ASN][1000 genomes]
rs7935673	0.83[ASN][1000 genomes]
rs960909	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv896987	chr11:9759918-9885849	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	esv3384280	chr11:9766350-9911228	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1996794	SWAP70	cis	multi-tissue	Pritchard
rs1996794	OVCH2	cis	cerebellum	SCAN
rs1996794	OR52E6	cis	parietal	SCAN
rs1996794	ILK	cis	cerebellum	SCAN
rs1996794	SWAP70	Cis_1M	lymphoblastoid	RTeQTL
rs1996794	SWAP70	cis	lymphoblastoid	seeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9799600-9823400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr11:9800200-9823800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:9801600-9823800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:9803000-9823400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr11:9803000-9823400	Weak transcription	Psoas Muscle	Psoas
6	chr11:9803200-9828600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:9803200-9828600	Weak transcription	Gastric	stomach
8	chr11:9803200-9828800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr11:9806800-9828600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr11:9807200-9823200	Weak transcription	Fetal Heart	heart
11	chr11:9808400-9828800	Weak transcription	Fetal Kidney	kidney
12	chr11:9809600-9823000	Weak transcription	HMEC	breast
13	chr11:9809600-9828600	Weak transcription	Esophagus	oesophagus
14	chr11:9809600-9832600	Weak transcription	Colonic Mucosa	Colon
15	chr11:9809800-9823200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr11:9809800-9828000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr11:9809800-9828600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr11:9810000-9823200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr11:9810000-9823200	Weak transcription	NH-A	brain
20	chr11:9810000-9829200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr11:9810200-9822600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr11:9810200-9828400	Weak transcription	Primary T cells from cord blood	blood
23	chr11:9810200-9829200	Weak transcription	Fetal Brain Male	brain
24	chr11:9810800-9823200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr11:9810800-9828600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr11:9810800-9829000	Weak transcription	Right Ventricle	heart
27	chr11:9811000-9828600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr11:9811200-9824000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr11:9811600-9822800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr11:9811600-9823000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr11:9811600-9823400	Weak transcription	Brain Hippocampus Middle	brain
32	chr11:9811600-9824000	Weak transcription	Brain Substantia Nigra	brain
33	chr11:9811600-9828000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr11:9811600-9828600	Weak transcription	Dnd41	blood
35	chr11:9811600-9828600	Weak transcription	HUVEC	blood vessel
36	chr11:9811600-9828800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr11:9811600-9828800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr11:9811800-9822600	Weak transcription	Colon Smooth Muscle	Colon
39	chr11:9811800-9823200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr11:9811800-9823200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr11:9811800-9823200	Weak transcription	Brain Anterior Caudate	brain
42	chr11:9811800-9823200	Weak transcription	Fetal Muscle Leg	muscle
43	chr11:9811800-9823200	Weak transcription	NHEK	skin
44	chr11:9811800-9823400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr11:9811800-9823400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr11:9811800-9827200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr11:9811800-9827800	Weak transcription	Fetal Thymus	thymus
48	chr11:9811800-9827800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr11:9811800-9828400	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr11:9811800-9828600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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