Variant report

Variant	rs11539
Chromosome Location	chr12:10374719-10374720
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:10372534-10377685	Hela-S3	cervix:	n/a	n/a
2	SP1	chr12:10374675-10375152	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr12:10374600-10374750	HMEC	breast:	n/a	n/a
4	POLR2A	chr12:10374583-10377702	IMR90	lung:	n/a	n/a
5	POLR2A	chr12:10372283-10377246	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:10373969..10375781-chr12:10380719..10382478,2	K562	blood:

Variant related genes	Relation type
KLRD1	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10505754	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap]
rs10734822	1.00[CEU][hapmap]
rs10734823	1.00[CEU][hapmap]
rs10734824	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap]
rs10743876	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10743878	1.00[CEU][hapmap]
rs10743879	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap]
rs10743880	1.00[CEU][hapmap]
rs10772244	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10772246	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10845098	1.00[CEU][hapmap]
rs11053719	1.00[CEU][hapmap]
rs2045881	1.00[CEU][hapmap]
rs2417582	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2417584	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2417585	1.00[CEU][hapmap]
rs2417586	1.00[CEU][hapmap]
rs2537782	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap]
rs2537800	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap]
rs2537801	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs2900385	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4267162	1.00[CEU][hapmap]
rs4372546	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap]
rs4483689	1.00[CEU][hapmap]
rs4764332	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4764333	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4764337	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4764342	0.84[EUR][1000 genomes]
rs4764359	1.00[CEU][hapmap]
rs59389382	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59511495	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59761822	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6488277	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap]
rs6488279	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs7302157	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7302532	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73060068	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73060081	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73062005	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7315203	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7959312	1.00[CEU][hapmap]
rs7960272	1.00[CEU][hapmap]
rs7962426	1.00[CEU][hapmap]
rs7974717	1.00[CEU][hapmap]

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	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1054811	chr12:10350587-10440005	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10366800-10386600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:10368000-10375400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:10368400-10377000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:10368400-10378400	Weak transcription	Fetal Heart	heart
5	chr12:10368400-10378600	Weak transcription	Stomach Mucosa	stomach
6	chr12:10368400-10380200	Weak transcription	GM12878-XiMat	blood
7	chr12:10368400-10380400	Weak transcription	Dnd41	blood
8	chr12:10368800-10375000	Strong transcription	Fetal Intestine Small	intestine
9	chr12:10369000-10376000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:10369000-10376600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:10369000-10377800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:10369200-10377200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:10369400-10377000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:10369400-10377600	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:10370000-10377200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:10370200-10376600	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr12:10370200-10377200	Strong transcription	Fetal Stomach	stomach
18	chr12:10370400-10376600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr12:10370600-10376600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr12:10370600-10377000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:10370600-10377000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:10370600-10377200	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr12:10370600-10377200	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr12:10370600-10377200	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:10370600-10377200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr12:10370600-10377200	Strong transcription	Stomach Smooth Muscle	stomach
27	chr12:10370600-10377600	Strong transcription	Fetal Muscle Leg	muscle
28	chr12:10370800-10376800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:10371200-10375200	Strong transcription	Thymus	Thymus
30	chr12:10371200-10376800	Strong transcription	Placenta Amnion	Placenta Amnion
31	chr12:10371200-10377200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
32	chr12:10371200-10377600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:10371400-10376600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr12:10371400-10377600	Strong transcription	Ovary	ovary
35	chr12:10371600-10376400	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr12:10371600-10377000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:10371600-10377200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr12:10371600-10377200	Strong transcription	Lung	lung
39	chr12:10371600-10377600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:10371800-10374800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr12:10371800-10376200	Strong transcription	Fetal Thymus	thymus
42	chr12:10371800-10376400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr12:10371800-10376600	Strong transcription	Brain Germinal Matrix	brain
44	chr12:10371800-10376600	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:10371800-10377000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr12:10371800-10377000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:10371800-10377000	Strong transcription	Fetal Muscle Trunk	muscle
48	chr12:10371800-10377000	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr12:10371800-10377200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr12:10371800-10377200	Strong transcription	Fetal Brain Female	brain

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