Variant report

Variant	rs2329611
Chromosome Location	chr7:40008949-40008950
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:39999018..40002091-chr7:40005223..40009207,3	K562	blood:
2	chr7:39988793..39991340-chr7:40008054..40010425,3	MCF-7	breast:
3	chr7:39989510..39991644-chr7:40006968..40009873,3	K562	blood:

Variant related genes	Relation type
ENSG00000065883	Chromatin interaction
ENSG00000259826	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10046564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10224206	0.95[EUR][1000 genomes]
rs10225492	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10228596	1.00[CHB][hapmap]
rs10234693	0.82[CEU][hapmap]
rs10235989	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10239324	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10246466	0.81[CEU][hapmap]
rs10247292	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253590	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10272514	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10272641	0.81[CEU][hapmap]
rs10275761	0.82[CEU][hapmap]
rs10277422	1.00[CHB][hapmap]
rs10277853	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10279016	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1082023	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1257699	0.82[CEU][hapmap]
rs12701787	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13231977	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13239106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13241453	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13310449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13310480	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17434388	1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs17435812	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17496226	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17496247	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17526699	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052097	0.81[CEU][hapmap]
rs2140254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492942	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28547436	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28638437	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34326687	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34470312	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34748607	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35052806	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35082351	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35226291	0.81[EUR][1000 genomes]
rs35618050	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4273753	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4428576	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4481477	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4498451	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947071	0.83[EUR][1000 genomes]
rs73127832	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73127862	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs731847	0.82[CEU][hapmap]
rs773382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773393	0.81[CEU][hapmap]
rs773402	0.82[CEU][hapmap]
rs773424	0.81[CEU][hapmap]
rs7780996	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7794792	0.81[EUR][1000 genomes]
rs7797041	0.81[CEU][hapmap]
rs7799846	0.81[CEU][hapmap]
rs7811585	0.81[EUR][1000 genomes]
rs809558	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs878785	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9639817	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9639820	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9655036	1.00[CHB][hapmap]
rs9655407	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9690347	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9986996	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9986997	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887973	chr7:39772654-40110720	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	nsv887975	chr7:39858378-40124137	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	nsv887976	chr7:39874986-40018693	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv887977	chr7:39885541-40018693	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv1015322	chr7:40006195-40141195	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	esv2761319	chr7:40006195-40142139	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39993600-40048200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:39994200-40027200	Weak transcription	HSMM	muscle
3	chr7:39994600-40009000	Weak transcription	HMEC	breast
4	chr7:39994800-40018000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr7:39995000-40009000	Weak transcription	Osteobl	bone
6	chr7:39995000-40018200	Weak transcription	Spleen	Spleen
7	chr7:39995200-40009000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:39995200-40010400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr7:39995200-40042600	Weak transcription	K562	blood
10	chr7:39996800-40014800	Weak transcription	Right Ventricle	heart
11	chr7:39996800-40016600	Weak transcription	Gastric	stomach
12	chr7:39997200-40015200	Weak transcription	Small Intestine	intestine
13	chr7:39997800-40027400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr7:39998000-40027200	Weak transcription	Hela-S3	cervix
15	chr7:39998200-40009000	Weak transcription	Brain Angular Gyrus	brain
16	chr7:39998200-40009800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:39998200-40010400	Weak transcription	Colon Smooth Muscle	Colon
18	chr7:39998200-40013400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr7:39998400-40010200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr7:39999800-40013600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr7:40000400-40016600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr7:40000600-40011400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr7:40001000-40009600	Weak transcription	Ovary	ovary
24	chr7:40001000-40010800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr7:40001000-40016600	Weak transcription	Dnd41	blood
26	chr7:40001000-40018600	Weak transcription	Thymus	Thymus
27	chr7:40001200-40009000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:40001200-40009200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr7:40001200-40014800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr7:40001200-40016800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr7:40001200-40018200	Weak transcription	Fetal Thymus	thymus
32	chr7:40005600-40009000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr7:40005600-40021000	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr7:40005600-40021000	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr7:40006200-40009600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr7:40006200-40015000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr7:40006600-40009200	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr7:40006600-40009600	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr7:40006600-40011400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr7:40006600-40018200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr7:40006600-40019800	Enhancers	Primary B cells from peripheral blood	blood
42	chr7:40006800-40031200	Weak transcription	Fetal Stomach	stomach
43	chr7:40007000-40009000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr7:40007000-40011400	Weak transcription	Liver	Liver
45	chr7:40007000-40014600	Weak transcription	Fetal Intestine Small	intestine
46	chr7:40007000-40014800	Weak transcription	Left Ventricle	heart
47	chr7:40007000-40014800	Weak transcription	Psoas Muscle	Psoas
48	chr7:40007200-40009000	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr7:40007200-40010800	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr7:40007200-40017400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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