Variant report

Variant	rs12195964
Chromosome Location	chr6:30790481-30790482
allele	G/T
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:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30687583..30690453-chr6:30788279..30790519,3	MCF-7	breast:
2	chr6:30788846..30792943-chr6:30842643..30845954,4	K562	blood:
3	chr6:30719066..30719985-chr6:30790233..30791190,3	MCF-7	breast:
4	chr6:30690499..30693062-chr6:30788565..30790679,2	MCF-7	breast:
5	chr6:30703666..30722133-chr6:30776009..30801352,184	MCF-7	breast:
6	chr6:30735902..30738522-chr6:30790223..30792279,2	MCF-7	breast:
7	chr6:30735402..30739247-chr6:30785239..30791444,10	MCF-7	breast:
8	chr6:30789581..30790517-chr6:31055362..31055927,3	K562	blood:
9	chr6:30780598..30803497-chr6:30842531..30855110,80	MCF-7	breast:
10	chr6:30710229..30713248-chr6:30788195..30791151,4	K562	blood:
11	chr6:30694636..30696358-chr6:30788592..30791356,2	K562	blood:
12	chr6:30687910..30689518-chr6:30789768..30791672,2	MCF-7	breast:
13	chr6:30789979..30790619-chr6:30852914..30853522,2	MCF-7	breast:
14	chr6:30787837..30792214-chr6:30792255..30797817,7	K562	blood:
15	chr6:30709253..30713765-chr6:30784905..30790853,10	K562	blood:
16	chr6:30703055..30723531-chr6:30783853..30800217,151	MCF-7	breast:
17	chr6:30723362..30725478-chr6:30789187..30791435,2	MCF-7	breast:
18	chr6:30784327..30791562-chr6:30848580..30853873,26	MCF-7	breast:
19	chr6:30787789..30791714-chr6:30792255..30797305,10	K562	blood:

No data

Variant related genes	Relation type
ENSG00000204580	Chromatin interaction
ENSG00000201988	Chromatin interaction
ENSG00000272540	Chromatin interaction
ENSG00000237775	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000263608	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000272273	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10807071	0.85[EUR][1000 genomes]
rs12189560	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12189986	0.84[EUR][1000 genomes]
rs12190453	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190527	0.88[AFR][1000 genomes]
rs12192205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192430	0.84[EUR][1000 genomes]
rs12192704	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192760	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12192828	0.85[EUR][1000 genomes]
rs12195469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195508	0.85[EUR][1000 genomes]
rs12195605	0.82[EUR][1000 genomes]
rs12197221	0.85[EUR][1000 genomes]
rs12198723	0.85[EUR][1000 genomes]
rs12199559	0.84[EUR][1000 genomes]
rs12199612	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12200562	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12200829	0.84[EUR][1000 genomes]
rs12202570	0.84[EUR][1000 genomes]
rs12202778	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12202957	0.84[EUR][1000 genomes]
rs12203011	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12203199	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12203797	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205844	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12205961	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12206022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206742	0.84[EUR][1000 genomes]
rs12206930	0.82[EUR][1000 genomes]
rs12207652	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12208098	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12208771	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12209725	0.84[EUR][1000 genomes]
rs12210111	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12210318	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12210590	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12212837	0.85[EUR][1000 genomes]
rs12213493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213497	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214232	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12214398	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12215119	0.85[EUR][1000 genomes]
rs16897921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16897932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17189483	0.96[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17189490	0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17195830	0.83[EUR][1000 genomes]
rs17195837	0.83[EUR][1000 genomes]
rs2394414	0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs28744161	0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs28744171	0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs28830248	0.84[AFR][1000 genomes]
rs28877339	0.82[EUR][1000 genomes]
rs28890780	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28896520	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4248152	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4327730	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4711240	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4711241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713373	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4713376	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4713386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713388	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4995774	0.80[AFR][1000 genomes]
rs59293911	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62400964	0.85[EUR][1000 genomes]
rs62400965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400977	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs62400978	0.85[EUR][1000 genomes]
rs62400979	0.84[EUR][1000 genomes]
rs62400980	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs62400981	0.85[EUR][1000 genomes]
rs62408707	0.81[EUR][1000 genomes]
rs62408708	0.82[EUR][1000 genomes]
rs62408709	0.96[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62408713	0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62408715	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62408716	0.84[EUR][1000 genomes]
rs62408717	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62408723	0.84[EUR][1000 genomes]
rs62408724	0.84[EUR][1000 genomes]
rs62408725	0.84[EUR][1000 genomes]
rs62408726	0.84[EUR][1000 genomes]
rs62408727	0.84[EUR][1000 genomes]
rs62408728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
6	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
8	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12195964	PACSIN1	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30779000-30794800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:30779000-30795800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:30782000-30796000	Weak transcription	Pancreas	Pancrea
4	chr6:30782000-30797000	Weak transcription	Gastric	stomach
5	chr6:30782800-30794600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:30783400-30794600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:30785400-30790800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:30786200-30790800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:30786400-30790800	Enhancers	HSMMtube	muscle
10	chr6:30786400-30791400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:30786400-30792800	Enhancers	Stomach Mucosa	stomach
12	chr6:30787400-30792200	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr6:30787600-30791000	Enhancers	Colonic Mucosa	Colon
14	chr6:30787800-30791400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr6:30788200-30791400	Weak transcription	Thymus	Thymus
16	chr6:30788200-30792400	Weak transcription	Spleen	Spleen
17	chr6:30788200-30794800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:30788200-30794800	Weak transcription	Esophagus	oesophagus
19	chr6:30788400-30791000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:30788400-30795800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:30788400-30796000	Weak transcription	Lung	lung
22	chr6:30788600-30790800	Enhancers	Hela-S3	cervix
23	chr6:30788600-30791400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:30788600-30794800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:30788600-30794800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:30788600-30795800	Weak transcription	Left Ventricle	heart
27	chr6:30788600-30795800	Weak transcription	Right Ventricle	heart
28	chr6:30788800-30795800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr6:30789200-30791200	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr6:30789200-30791800	Enhancers	Placenta	Placenta
31	chr6:30789200-30792800	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr6:30789400-30790600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:30789400-30790600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:30789400-30790800	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr6:30789400-30790800	Enhancers	Small Intestine	intestine
36	chr6:30789400-30790800	Enhancers	Osteobl	bone
37	chr6:30789400-30793000	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr6:30789600-30790600	Enhancers	Fetal Lung	lung
39	chr6:30789600-30790600	Enhancers	NH-A	brain
40	chr6:30789600-30790800	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr6:30789600-30790800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:30789600-30790800	Enhancers	Muscle Satellite Cultured Cells	--
43	chr6:30789600-30790800	Enhancers	Adipose Nuclei	Adipose
44	chr6:30789600-30790800	Enhancers	Brain Hippocampus Middle	brain
45	chr6:30789600-30790800	Enhancers	Brain Substantia Nigra	brain
46	chr6:30789600-30790800	Enhancers	Fetal Heart	heart
47	chr6:30789600-30790800	Enhancers	Fetal Intestine Large	intestine
48	chr6:30789600-30790800	Enhancers	Fetal Thymus	thymus
49	chr6:30789600-30790800	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr6:30789600-30790800	Flanking Active TSS	A549	lung

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