Variant report

Variant	rs9652840
Chromosome Location	chr17:37929428-37929429
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:37924711..37926315-chr17:37927219..37929986,2	MCF-7	breast:
2	chr17:37926557..37928473-chr17:37928969..37931505,2	K562	blood:
3	chr17:37928224..37930881-chr17:37931679..37935792,4	K562	blood:
4	chr17:37910518..37912033-chr17:37928205..37930091,2	K562	blood:
5	chr17:37927328..37929448-chr17:38082417..38083917,2	MCF-7	breast:
6	chr17:37908791..37912830-chr17:37925750..37930091,5	K562	blood:

Variant related genes	Relation type
ENSG00000161405	Chromatin interaction
ENSG00000172057	Chromatin interaction

Extended variants
information (count: 142 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs12709364	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12937330	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12938117	1.00[EUR][1000 genomes]
rs12938617	0.96[EUR][1000 genomes]
rs12938749	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12940616	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12942660	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12945253	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12946040	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12946188	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12946792	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12947480	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12952146	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13313561	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13313564	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13313573	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13380871	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1453560	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1510475	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16965367	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17676923	0.83[EUR][1000 genomes]
rs2313429	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28392589	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28403951	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28449671	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28535471	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28537796	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28580691	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28621669	1.00[EUR][1000 genomes]
rs28648398	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28661421	1.00[EUR][1000 genomes]
rs28695941	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28723017	1.00[EUR][1000 genomes]
rs28842324	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28880017	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28896477	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2941509	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3169572	1.00[CEU][hapmap]
rs34016964	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34053394	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34291217	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34344462	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34485135	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34518282	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34582264	0.88[EUR][1000 genomes]
rs34599546	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34640000	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34654193	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34758895	0.92[EUR][1000 genomes]
rs34864615	0.96[EUR][1000 genomes]
rs34925681	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34988504	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35088469	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35105110	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35130019	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35336365	0.86[EUR][1000 genomes]
rs35352075	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35397078	0.88[EUR][1000 genomes]
rs35405174	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35506518	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35938199	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36097841	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4252665	1.00[CEU][hapmap]
rs4337325	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4622539	1.00[EUR][1000 genomes]
rs56928975	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58075375	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66763967	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67135646	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67571561	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67600807	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67605703	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71369788	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71369791	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71369792	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7211998	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7217133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7224641	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73302152	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73304123	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7503018	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8067523	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8068125	1.00[EUR][1000 genomes]
rs8068894	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8069531	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8069893	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8072612	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8076347	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8078409	0.88[EUR][1000 genomes]
rs8079075	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9652838	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9891131	1.00[CEU][hapmap]
rs9892781	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9894370	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9894680	1.00[EUR][1000 genomes]
rs9894898	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9896940	1.00[CEU][hapmap]
rs9898031	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9898464	1.00[EUR][1000 genomes]
rs9899006	1.00[EUR][1000 genomes]
rs9899336	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9899345	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9900019	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9900538	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9900541	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9901483	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9901617	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9901917	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9902621	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9904277	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9904834	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9905881	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9907096	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9907291	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9907564	1.00[EUR][1000 genomes]
rs9907794	1.00[EUR][1000 genomes]
rs9907966	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9907988	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9908694	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9908983	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9909365	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9909432	0.89[EUR][1000 genomes]
rs9910678	1.00[CEU][hapmap]
rs9911069	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9911634	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9911669	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9911688	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9912095	1.00[EUR][1000 genomes]
rs9913044	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9913596	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9913769	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9913795	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9913957	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9914302	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9914516	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs9914665	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9914757	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9915509	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9915797	0.92[EUR][1000 genomes]
rs9916259	1.00[CEU][hapmap];1.00[EUR][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	nsv1064787	chr17:37892843-38054410	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv543342	chr17:37892843-38054410	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37912000-37930400	Weak transcription	Esophagus	oesophagus
2	chr17:37920000-37930000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr17:37920800-37931000	Genic enhancers	Primary B cells from peripheral blood	blood
4	chr17:37924600-37929600	Enhancers	Duodenum Mucosa	Duodenum
5	chr17:37925400-37929600	Enhancers	Dnd41	blood
6	chr17:37925600-37938400	Weak transcription	Pancreas	Pancrea
7	chr17:37927200-37930400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr17:37927400-37930400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr17:37927400-37931000	Genic enhancers	Fetal Thymus	thymus
10	chr17:37928000-37931000	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr17:37928200-37929800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
12	chr17:37928400-37930400	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr17:37928400-37930600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr17:37928600-37929800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr17:37928600-37930200	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr17:37928800-37929600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr17:37928800-37929800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr17:37928800-37929800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr17:37928800-37930200	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr17:37928800-37930600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr17:37929000-37930200	Enhancers	Thymus	Thymus
22	chr17:37929000-37930400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr17:37929200-37929600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr17:37929200-37929600	Enhancers	Spleen	Spleen
25	chr17:37929400-37929600	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
26	chr17:37929400-37929600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr17:37929400-37929600	Enhancers	Colonic Mucosa	Colon
28	chr17:37929400-37929600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr17:37929400-37929800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr17:37929400-37930400	Enhancers	Primary hematopoietic stem cells	blood
31	chr17:37929400-37930800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr17:37929400-37931200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
33	chr17:37929400-37931400	Genic enhancers	Primary B cells from cord blood	blood
34	chr17:37929400-37932000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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