Variant report

Variant	rs3129792
Chromosome Location	chr6:28956416-28956417
allele	A/G
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:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28914281..28916611-chr6:28956056..28957643,2	K562	blood:
2	chr6:28926035..28928870-chr6:28956157..28957921,2	K562	blood:
3	chr6:28915108..28916611-chr6:28956143..28957725,2	K562	blood:
4	chr6:28955433..28959890-chr6:28970874..28974365,4	MCF-7	breast:
5	chr6:28805954..28808293-chr6:28955372..28957939,3	K562	blood:
6	chr6:28891456..28893478-chr6:28954362..28956726,2	K562	blood:
7	chr6:28955940..28958074-chr6:28964364..28967031,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf100-3	chr6:28956077-28956581	NONHSAT108500

No data

Variant related genes	Relation type
ENSG00000197935	Chromatin interaction
ENSG00000225173	Chromatin interaction
ENSG00000204713	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs1002925	0.83[EUR][1000 genomes]
rs1005123	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1237485	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1476016	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1543796	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs169683	0.82[EUR][1000 genomes]
rs1794587	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs184093	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2013848	0.92[ASN][1000 genomes]
rs2032500	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2071785	0.91[ASN][1000 genomes]
rs2071790	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs209122	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs209126	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs209128	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs209129	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs209137	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs209138	0.86[EUR][1000 genomes]
rs209148	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs209149	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs209152	0.82[EUR][1000 genomes]
rs209153	0.85[EUR][1000 genomes]
rs209160	0.83[EUR][1000 genomes]
rs209161	0.85[EUR][1000 genomes]
rs209163	0.85[EUR][1000 genomes]
rs209164	0.82[EUR][1000 genomes]
rs209176	0.83[EUR][1000 genomes]
rs209184	0.83[EUR][1000 genomes]
rs209186	0.82[EUR][1000 genomes]
rs2157312	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2157313	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2179648	0.94[ASN][1000 genomes]
rs2187807	0.92[ASN][1000 genomes]
rs2187808	0.92[ASN][1000 genomes]
rs2206040	0.91[AFR][1000 genomes]
rs2206041	0.91[AFR][1000 genomes]
rs2208536	0.82[EUR][1000 genomes]
rs2269555	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2394512	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2394548	0.91[AFR][1000 genomes]
rs2754764	0.82[EUR][1000 genomes]
rs2754767	0.82[EUR][1000 genomes]
rs2765218	0.81[EUR][1000 genomes]
rs2765219	0.82[EUR][1000 genomes]
rs2765229	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3116844	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3129145	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3129150	0.82[AMR][1000 genomes]
rs3129793	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130718	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3130841	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3130842	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3130886	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3130889	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3130897	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3131070	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3131074	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3131077	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3131102	0.89[EUR][1000 genomes]
rs3131342	0.82[EUR][1000 genomes]
rs3132386	0.83[EUR][1000 genomes]
rs3135303	0.85[EUR][1000 genomes]
rs3135315	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3135319	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3135321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3135322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3135323	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3135324	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3135326	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3135327	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3135328	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs377392	0.83[EUR][1000 genomes]
rs381808	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs386628	0.83[EUR][1000 genomes]
rs393431	0.83[EUR][1000 genomes]
rs4427026	0.92[ASN][1000 genomes]
rs4713186	0.89[ASN][1000 genomes]
rs4713187	0.89[ASN][1000 genomes]
rs4713188	0.90[ASN][1000 genomes]
rs4713190	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4713192	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4947339	0.92[ASN][1000 genomes]
rs6456876	0.92[ASN][1000 genomes]
rs6456880	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6456883	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6456891	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6900967	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6901599	0.92[ASN][1000 genomes]
rs6904975	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6906909	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6914955	0.91[ASN][1000 genomes]
rs6916161	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6920392	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6931823	0.92[ASN][1000 genomes]
rs719746	0.91[AFR][1000 genomes]
rs763009	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7743189	0.91[ASN][1000 genomes]
rs7761547	0.92[ASN][1000 genomes]
rs7768299	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9257401	0.92[ASN][1000 genomes]
rs9257404	0.91[ASN][1000 genomes]
rs9257405	0.90[ASN][1000 genomes]
rs9257408	0.82[ASN][1000 genomes]
rs9257421	0.90[ASN][1000 genomes]
rs9257447	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9257449	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9257455	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9257461	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9257464	0.85[ASN][1000 genomes]
rs9348816	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9348817	0.80[AMR][1000 genomes]
rs9380109	0.83[AFR][1000 genomes]
rs9393939	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9468467	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9468472	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9468480	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
3	nsv1023540	chr6:28922691-29326018	Active TSS Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
4	nsv538169	chr6:28922691-29326018	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv869541	chr6:28922692-29326017	Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv916439	chr6:28922697-29326087	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv462668	chr6:28922719-29342775	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	nsv601213	chr6:28922719-29342775	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv1015796	chr6:28923980-29342825	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv462669	chr6:28936556-29337500	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
11	nsv601214	chr6:28936556-29337500	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
12	nsv601215	chr6:28946920-29348297	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv1023028	chr6:28956136-29343575	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
14	nsv538170	chr6:28956136-29343575	ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
15	nsv1018937	chr6:28956136-29366175	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3129792	ZKSCAN3	cis	cerebellum	SCAN
rs3129792	NKAPL	cis	parietal	SCAN
rs3129792	HIST1H2BH	cis	cerebellum	SCAN
rs3129792	ZSCAN23	cis	cerebellum	SCAN
rs3129792	ZNF323	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28955800-28957000	Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr6:28955800-28957200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:28955800-28957200	Active TSS	H1 Cell Line	embryonic stem cell
4	chr6:28955800-28957200	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr6:28955800-28957200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr6:28955800-28957200	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr6:28956000-28956600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr6:28956000-28956600	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr6:28956000-28956600	Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr6:28956000-28956600	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:28956000-28956600	Bivalent Enhancer	Brain Cingulate Gyrus	brain
12	chr6:28956000-28956600	Flanking Bivalent TSS/Enh	Thymus	Thymus
13	chr6:28956000-28956600	Active TSS	HSMM	muscle
14	chr6:28956000-28956800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:28956000-28956800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:28956000-28956800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:28956000-28956800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
18	chr6:28956000-28956800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
19	chr6:28956000-28956800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
20	chr6:28956000-28956800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:28956000-28956800	Active TSS	Muscle Satellite Cultured Cells	--
22	chr6:28956000-28956800	Bivalent/Poised TSS	Cortex derived primary cultured neurospheres	brain
23	chr6:28956000-28956800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:28956000-28956800	Bivalent/Poised TSS	Fetal Stomach	stomach
25	chr6:28956000-28956800	Active TSS	Psoas Muscle	Psoas
26	chr6:28956000-28956800	Active TSS	Right Ventricle	heart
27	chr6:28956000-28956800	Active TSS	NH-A	brain
28	chr6:28956000-28956800	Active TSS	NHLF	lung
29	chr6:28956000-28956800	Active TSS	Osteobl	bone
30	chr6:28956000-28957000	Active TSS	H9 Cell Line	embryonic stem cell
31	chr6:28956000-28957000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:28956000-28957000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr6:28956000-28957000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr6:28956000-28957000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:28956000-28957000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:28956000-28957000	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
37	chr6:28956000-28957000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:28956000-28957000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:28956000-28957000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:28956000-28957000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
41	chr6:28956000-28957000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
42	chr6:28956000-28957000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
43	chr6:28956000-28957000	Active TSS	Fetal Kidney	kidney
44	chr6:28956000-28957000	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr6:28956000-28957000	Active TSS	NHEK	skin
46	chr6:28956000-28957200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:28956000-28957200	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr6:28956000-28957200	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr6:28956000-28957200	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr6:28956000-28957200	Active TSS	K562	blood

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