Variant report

Variant	rs2744968
Chromosome Location	chr6:34584951-34584952
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:34584121..34585997-chr6:34662703..34665284,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PACSIN1-2	chr6:34584315-34585035	NONHSAT112140

Variant related genes	Relation type
ENSG00000272288	Chromatin interaction
ENSG00000196821	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11970421	0.93[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs16894102	0.81[CHB][hapmap]
rs1964810	0.89[ASN][1000 genomes]
rs2064253	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2235571	0.90[ASN][1000 genomes]
rs2235572	0.94[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs2252551	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2294536	0.95[ASN][1000 genomes]
rs2492862	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2744948	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2744952	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2744953	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2744962	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2744963	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2744966	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2744967	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2744970	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2744975	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2764199	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs2814950	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap]
rs2814989	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2814990	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2814997	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2814998	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2815000	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2815003	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3798349	0.80[CHB][hapmap]
rs3800456	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41438444	0.82[ASN][1000 genomes]
rs4615374	0.91[ASN][1000 genomes]
rs4618513	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711399	0.81[EUR][1000 genomes]
rs56987113	0.88[ASN][1000 genomes]
rs57994417	0.95[ASN][1000 genomes]
rs58643640	0.85[ASN][1000 genomes]
rs6932930	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[EUR][1000 genomes]
rs6939345	1.00[CEU][hapmap];0.80[CHB][hapmap]
rs7752237	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7772600	0.82[ASN][1000 genomes]
rs9296126	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9368829	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9380451	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[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	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv2758046	chr6:34382492-34714677	Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2759418	chr6:34382492-34714677	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv885785	chr6:34404636-34874002	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv1033583	chr6:34471572-34828372	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv885792	chr6:34507311-34607958	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv885793	chr6:34520267-34886436	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv823667	chr6:34533015-34592524	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv830640	chr6:34542489-34714677	Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
11	nsv885794	chr6:34561585-34673149	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv1032557	chr6:34565802-34802008	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
13	nsv538196	chr6:34565802-34802008	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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	33 gene(s)	inside rSNPs	diseases
14	esv2763967	chr6:34566255-34925463	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
15	nsv981134	chr6:34584017-34585112	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2744968	SNRPC	Cis_1M	lymphoblastoid	RTeQTL
rs2744968	UHRF1BP1	cis	Adipose Subcutaneous	GTEx
rs2744968	UHRF1BP1	cis	Artery Tibial	GTEx
rs2744968	UHRF1BP1	cis	Whole Blood	GTEx
rs2744968	C6orf107	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34556200-34612200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:34557400-34612400	Weak transcription	Fetal Kidney	kidney
3	chr6:34562600-34585200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:34567000-34612200	Weak transcription	Fetal Lung	lung
5	chr6:34567800-34612400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:34570400-34612600	Weak transcription	Brain Anterior Caudate	brain
7	chr6:34570600-34610000	Weak transcription	Brain Hippocampus Middle	brain
8	chr6:34570800-34587000	Weak transcription	Brain Substantia Nigra	brain
9	chr6:34570800-34618800	Weak transcription	Brain Angular Gyrus	brain
10	chr6:34571000-34585200	Weak transcription	Right Ventricle	heart
11	chr6:34571000-34621400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr6:34571000-34624000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:34572400-34612600	Weak transcription	Aorta	Aorta
14	chr6:34573800-34607200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:34574400-34612400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr6:34574400-34623400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr6:34574600-34585200	Weak transcription	Ovary	ovary
18	chr6:34574600-34598200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:34574600-34598200	Weak transcription	Lung	lung
20	chr6:34574600-34612600	Weak transcription	Gastric	stomach
21	chr6:34574600-34613600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:34574600-34613600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:34574800-34590400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr6:34574800-34596400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:34574800-34596600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:34574800-34596600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:34574800-34611800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr6:34574800-34612200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr6:34574800-34612400	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr6:34574800-34612400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr6:34574800-34612600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:34574800-34613200	Weak transcription	Small Intestine	intestine
33	chr6:34575000-34612400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr6:34575000-34612400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr6:34575000-34612600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:34575000-34618800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr6:34575400-34606600	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr6:34575600-34611200	Weak transcription	Placenta	Placenta
39	chr6:34575800-34595000	Weak transcription	Fetal Thymus	thymus
40	chr6:34575800-34596600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr6:34575800-34612000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr6:34577400-34613400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr6:34577400-34618600	Weak transcription	Colon Smooth Muscle	Colon
44	chr6:34578800-34592200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr6:34578800-34598400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr6:34578800-34612400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr6:34579200-34614200	Weak transcription	Pancreas	Pancrea
48	chr6:34579400-34597400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr6:34579400-34597400	Weak transcription	HMEC	breast
50	chr6:34579400-34597400	Weak transcription	NHDF-Ad	bronchial

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